Open Journal of Genetics, 2013, 3, 9-86 OJGen
http://dx.doi.org/10.4236/ojgen.2013.32A2002 Published Online July 2013 (http://www.scirp.org/journal/ojgen/)
UP780, a Chromone-Enriched Aloe Composition, Enhances
Adipose Insulin Receptor Signaling and Decreases Liver
Lipid Biosynthesis
Julie Tseng-Crank1*, Seon-Gil Do2, Brandon Corneliusen1, Carmen Hertel1, Jennifer Homan1,
Mesfin Yimam1, Jifu Zhao1, Qi Jia1
1Unigen, Seattle, USA
2Unigen Korea, Songjung-Ri, Byeongchen-Myeon, Vheonan-Si, Chungnam, South Korea
Received 12 May 2013; revised 17 June 2013; accepted 17 July 2013
Copyright © 2013 Julie Tseng-Crank et al. This is an open access article distributed under the Creative Commons Attribution License,
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
ABSTRACT
Nutrigenomic studies were conducted to uncover the
mechanism of action for the hypoglycemic and insulin
sensitizing effects of UP780. From high fat diet-induc-
ed obesity mouse model for UP780, livers and white
adipose tissues (WAT) from groups of lean control,
high fat diet (HFD), and HFD treated with UP780 were
collected for microarray study. Microarray genera-
ted gene expression changes were applied to Ingenu-
ity Pathway Analysis for changes in canonical meta-
bolic and signaling pathways. Microarray was vali-
dated by quantitative reverse transcriptase-polyme-
rase chain reaction (QPCR), Western blots, liver tri-
glyceride, liver cholesterol, liver steatosis, and insulin
ELISA. UP780 treatment decreased liver gene expres-
sions for multiple enzymes involved in fatty acid bio-
synthesis and triglyceride production. UP780 treat-
ment increased gene expressions globally for the insu-
lin receptor signaling pathway in WAT. Both liver
triglyceride and liver cholesterol levels were signifi-
cantly reduced by UP780 over HFD. The reduction of
liver fat was confirmed by microscopic analysis of li-
ver steatosis. Finally, UP780 significantly decreased
fasting plasma insulin level over HFD. The mechani-
sm of action for UP780 indicated a reduction of liver
fat accumulation and an enhancement in adipose tis-
sue insulin signaling pathway. This provided mecha-
nistic explanation for the in vivo UP780 effects of en-
hanced insulin sensitiveity and decreased blood glu-
cose in mouse diabetes and prediabetes models.
Keywords: Nutrigenomics; Insulin Signaling Pathway;
Liver Fatty Acid Biosynthesis; Liver Steatosis; Aloe Vera
1. INTRODUCTION
Diabetes and prediabetes have become epidemic globally.
In recent US surveys, 26.9% of the population aged 65
years and older had diabetes and 35% of those 20 years
or older had prediabetes [1]. WHO of the United Nations
estimated in 2011 that 346 million people worldwide had
diabetes, and that number was likely to double by 2030
[2]. Complications of diabetes include heart disease,
stroke, hypertension, blindness, kidney disease, neuro-
pathy, amputation, and dental disease. Economic bur-
den of diabetes was high, in US, the 2007 direct and in-
direct cost of diabetes amounted to $174 billion [1].
The culprit for the epidemic of type II diabetes and
prediabetes/metabolic syndrome is obesity. Obesity pre-
disposes patients to a complex metabolic pathology, cha-
racterized by a cluster of closely related clinical fea-
tures of central obesity, hyperglycemia, insulin resistance,
dyslipidaemia and hypertension [3]. Metabolic syndrome
is associated with increased risk of type II diabetes and
cardiovascular disease; cardiovascular diseases ultima-
tely are responsible for a large proportion of diabetic
mortality [4]. The epidemics in type II diabetes calls for
interventions at the stage of metabolic syndrome, with
diet, exercise, and medications/dietary supplements tar-
geting insulin resistance, to decrease the societal burden
from diabetes.
For thousands of years, herbal medicine was the only
treatment available to mankind. What is old is not nec-
essarily worthless in the modern world. Recently, tradi-
tional herbal medicines with a history in diabetic treat-
ment, now as nutritional supplements or as alternate me-
dicines, were rediscovered by the medical world for obe-
sity, metabolic syndrome, and diabetes: Aloe vera leaf
gel [5], berberine [6,7], bitter melon [8], ginsenoside Rb1
*Corresponding author.

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 10
[9], genistein [10], and cinnamon [11], to name a few. In
addition, resveratrol from red grape was recently disco-
vered to improve obesity and aging related disorders
[12].
Aloe vera inner leaf gel and whole leaf extract had
been reported to produce a hypoglycemic effect in dia-
betic animal models of alloxan-induced diabetic mice
[13-15] and type I/type II diabetic rats [16,17]. UP780,
the Aloe vera inner leaf gel extract standardized with
aloesin, was found to decrease fasting blood glucose lev-
els and insulin resistance in mouse diet-induced obesity
(DIO) model and db diabetic model [18]. Significantly,
UP780 was the subject of a double blind, placebo con-
trolled clinical pilot study of prediabetic patients. After
eight weeks of treatment, UP780 significantly reduced
fasting blood glucose, insulin, HbA1c, fructosamine, and
urinary F2-isoprostanes compared to placebo [19].
Although aloe was traditionally used for diabetes
treatment, and shown to reduce blood glucose, improve
lipid profile, and provide anti-oxidants in diabetic animal
models [13,15-17,20,21], there is a paucity of aloe me-
chanism of action study. From the UP780 prediabetic
DIO mouse study [18], livers and white adipose tissues
(WAT) collected from the DIO animals were used in a
nutrigenomic study. By microarray/pathway analysis and
QPCR gene expression, UP780 decreased fatty acid bio-
synthesis and triglyceride production in liver and in-
creased insulin receptor signaling pathway in WAT. The
microarray and QPCR gene expression data was valida-
ted by Western blot, liver triglyceride/cholesterol, liver
steatosis, and plasma insulin ELISA.
2. MATERIALS AND METHODS
2.1. Composition of UP780
UP780 is a combination of Aloe vera inner leaf gel
powder (QMatrix®) standardized to contain 2% - 4% alo-
esin. QMatrix® is produced from Aloe vera gel car-
bon-filtered to remove anthraquinone, which has laxative
effect [22]. Aloesin, an aromatic chromone isolated from
Aloe ferox, was discovered by high throughput screening
of 2059 plant extracts to increase adiponectin secretion
from differentiated 3T3-L1 adipocytes [18]. In the pre-
paration of QMatrix®, aloesin was removed by carbon
filtration. Aloesin was added to QMatrix® with an expec-
tation of broadening the aloe action for glycemic control.
GW1929 is a specific non-thiazolidinedione, tyrosine-
derived agonist of peroxisome proliferatoractivated rece-
ptor gamma (PPARα, Tocris Bioscience). Thiazolidine-
dione class PPAR agonists are standard medicines for
type II diabetes [23].
2.2. Methods
Methods for tissue collection from DIO mice, RNA ex-
traction, microarray, Ingenuity Pathway Analysis, real-
time RT-QPCR, Western blot, liver triglyceride and cho-
lesterol assays, liver steatosis, and plasma insulin ELISA
are described in the supplemental materials.
3. RESULTS
3.1. Microarray/QPCR and UP780 Mechanism
of Action
HFD feeding of C57BL/6J mice is known to induce gene
expression variations in organs that respond to high ca-
loric intake such as liver, fat, and muscle [12]. It was of
great interest to observe the effects of UP780 treatment
over HFD-induced changes in gene expressions. Micro-
array gene expression variations were applied to the con-
struction of a hypothesis for UP780 mechanism of action,
based on the canonical metabolic and signaling pathway
analysis, and taken into account of known gene functions
[24,25]. The large volume of pathway analysis results
were allocated to the supplemental materials. Only key
genes involved in the interpretation of biological signi-
ficance of UP780 were validated by QPCR (Table 1). An
equivalent Table 2 was generated for WAT. Concordance
between liver microarray and liver QPCR was good, 11
out of 14, when the genes loosely categorized as Sig-
naling were not counted (Table 1) Concordance between
WAT microarray and QPCR was excellent, 11 out of the
13 key genes tested (Table 2)
The liver key gene list in Table 1 emphasized the me-
tabolic pathways. Liver responds to the nutritional state
of the body by modifying the enzyme/gene activities in-
volved in metabolism, either by protein phosphorylation
or by gene expression variation. With liver, genes encod-
ing relevant members of metabolic pathways of fatty
acid biosynthesis, fatty acid metabolism, glycollysis/glu-
coneogenesis, and fat transport were all found to be stri-
kingly up-regulated by HFD and down-regulated by
UP780 (Table 1). The hypoglycemic effect of UP780
suggested a decreased gluconeogenesis pathway. Many
genes in glycolysis/gluconeogenesis pathway were up-
regulated by HFD and down-regulated by UP780 (Table
1, Supplement Figure 5 and Supplement Table 1).
While this may suggest a decrease of gluconeogenesis by
UP780, close examination of the functions of the genes
involved indicated contradictions that cannot be resolved
by gene expression data alone. In particular, phosphoe-
nolpyruvate carboxykinase (PEPCK) is a rate-limiting
enzyme for gluconeogenesis. The cytosolic PEPCK1 was
up-regulated by HFD/UP780, opposing gluconeogenesis
as a mechanism of hypoglycemic control. Effect of
UP780 on carbohydrate metabolism in liver will need
further studies.
Strong evidence of UP780-modulated metabolic path-
ways in support of UP780 insulin-sensitiziing effect was

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 11
Table 1. Liver gene expression variations from microarray and QPCR. For microarray, up-regulations ≥ 0.8 and with a p-value <0.05
are highlighted with red and marked with “ +”, down-regulations ≤−0.8 and with a p-value < 0.05 are high- lighted with green and
marked by “  -”. For QPCR, up- and down-regulations over 2 fold difference are highlighted with red and green, respectively. Con-
cordances in between microarray and QPCR are marked with ●.
Microarray (Fold Change) QPCR (Relative Expression)
Genes Description LUP-LVLUP-LCLV-LCLC LV LUP
Fatty Acid Biosynthesis
ACC1 ACACA, Acetyl-CoA carboxylase 1  −1.80  −1.36  +1.32
ACC2 ACACB, Acetyl-CoA carboxylase 2  −3.11  −2.82  +1.101.00 ± 0.13 0.81 ± 0.06 0.33 ± 0.16●
ACSL3 Acyl-CoA synthetase long chain 3  −1.77  −1.43  +1.24
FASN Fatty acid synthase  −3.89 −2.53  +1.541.00 ± 0.02 0.93 ± 0.03 0.35 ± 0.01●
FADS1 Fatty acid desaturase 1  −1.90  −1.32  +1.43
FADS2 Fatty acid desaturase 2  −3.48  −1.32  +2.79
SCD1 Stearyl-CoA desaturase  −4.50 −4.25  +1.071.00 ± 0.00 0.98 ± 0.02 0.26 ± 0.01●
ELOV5 Elongation of long chain fatty acids 5  −2.44  −1.34  +1.83
ELOV6 Elongation of long chain fatty acids 6  −2.89 −2.39  +1.25
Fatty Acid Metabolism
ACOX1 Acyl-CoA oxidase 1, palmitoyl  −1.87  −1.15  +1.621.00 ± 0.01 1.12 ± 0.02 0.92 ± 0.02
ACOT1 Acyl-CoA thioesterase 1, peroxisome  −6.42 −3.26  +2.53
CPT1A Carnitine palmitoyl transferase 1A  −1.78  +1.21 +2.161.00 ± 0.04 1.43 ± 0.04 1.06 ± 0.05●
CRAT Carnitine acetyltransferase  −2.41  −1.10  +2.18
HAO2 Hydroxyacid oxidase 2, peroxisome  −2.33  −1.15  +2.03
Steroid Biosynthesis
FDPS Farnesyl diphosphate synthase  −1.39 −1.99  −1.43
HMGCR 3-Hydroxy-3-methylglutaryl-CoA reductase  −1.19 −2.26  −1.90 1.00 ± 0.03 0.41 ± 0.01 0.47 ± 0.01●
MVD Mevalonate decarboxylase  −2.70 −2.51  +1.07
Bile Acid Biosynthesis
CYP7A1 Cytochrome P450 7A1  +2.77 −2.45  −4.89 1.06 ± 0.42 0.07 ± 0.03 0.97 ± 0.02●
CYP7B1 Cytochrome P450 7B1  +2.76 +2.30 −1.22 1.00 ± 0.50 0.56 ± 0.02 2.53 ± 0.08●
Fat Transport
APOA4 Apolipoprotein A4, chylomicron  −3.48 +2.41 +8.40
CD36 Fat transporter  −3.29  −1.34  +2.451.00 ± 0.07 1.98 ± 0.08 0.98 ± 0.04●
FABP4 Fatty acid binding protein 4  +1.07 +2.70 +2.521.00 ± 0.04 0.54 ± 0.08 2.77 ± 0.03
FABP5 Fatty acid binding protein 5  +2.63 −1.49  −3.91 1.00 ± 0.06 0.08 ± 0.01 0.64 ± 0.14●
LDLR LDL receptor  −2.75  −1.54  +1.67
Glycolysis/Gluconeogenesis
ALDH1B1 Aldehyde dehydrogenase 1B1  −3.04 −1.77  +1.72
GCK Glucokinase, MODY2  −2.29  +1.13 +2.04
GYS2 Glycogen synthase 2  −1.40  +1.05 +1.471.00 ± 0.09 1.08 ± 0.06 1.14 ± 0.03
HK1 Hexokinase 1  −2.55 −1.77  −1.39
PDK4 Pyruvate dehydrogenase kinase 4  −2.59  −1.41  +1.831.03 ± 0.32 1.70 ± 0.44 0.11 ± 0.04●
PKLR Pyruvate kinase, liver & RBC  −2.26  −1.54  +1.62
PEPCK1 PCK1, Phosphoenolpyruvate carboxykinase 1  +1.09 +2.34 +2.231.00 ± 0.04 1.73 ± 0.05 2.72 ± 0.08●
Signaling
AMPKα2 PRKAA2, AMP-activated kinase α2  −1.60  −1.49  +1.071.00 ± 0.02 0.85 ± 0.13 0.96 ± 0.03
AMPKγ2 PRKAG2, AMP-activated kinaseγ2  −1.40  −1.38  −1.01 1.00 ± 0.05 0.79 ± 0.11 0.75 ± 0.01
SLC2A2 GLUT2, solute carrier family 2, member 2  −1.50  −1.37  +1.091.00 ± 0.02 0.84 ± 0.06 0.77 ± 0.04
HNF4A Hepatocyte nuclear factor 4α  −1.18  −1.27  −1.07 1.00 ± 0.04 0.74 ± 0.04 1.06 ± 0.04
mTOR FRAP1, FK506 binding protein 12, rapamycin-
associated protein 1  −1.10  +1.18 +1.431.00 ± 0.06 0.93 ± 0.01 0.88 ± 0.04
PGC1A PPARγ coactivator 1A  −1.66  −1.45  +1.221.46 ± 1.46 1.13 ± 0.79 2.53 ± 0.54
PGC1B PPARγ coactivator 1B  −2.32  −1.59  +1.461.08 ± 0.55 1.05 ± 0.26 1.32 ± 0.07
PPARα Peroxisome proliferator-activated receptor   −2.41  +1.07 +2.251.00 ± 0.09 1.42 ± 0.03 1.44 ± 0.05
PPARδ Peroxisome proliferators-activated receptor   −1.11  +1.07 +1.221.00 ± 0.05 1.12 ± 0.08 0.99 ± 0.14
SREBF1 Sterol regulatory element binding factor 1  −2.40  −1.58  +1.521.00 ± 0.09 0.92 ± 0.04 0.88 ± 0.09
LUP: Livers from UP780 treated DIO mice. LV: Livers from high fat diet, HFD, treated DIO mice. LC: Livers from lean control mice.

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 12
Table 2. WAT gene expression variations from microarray and QPCR. For microarray, up-regulations ≥ 0.8 and with a p-value < 0.05
are highlighted with red and marked with “ +”, down-regulations ≤−0.8 and with a p-value < 0.05 are highlighted with green and
marked with “ -”. For QPCR, up- and down-regulations over 2 fold difference are highlighted with red and green, respectively.
Concordances in between microarray and QPCR are marked with ●.
Microarray (Fold Change) QPCR (Relative Expression)
Gene Description
FUP/FVFUP/FCFV/FCFC FV FUP
Insulin Receptor Signaling
EIF4EBP1 Eeukaryotic translation initiation factor 4E  +2.16 +1.02 −2.23
binding protein 1
FOXO1 Forkhead box O1  +1.58 −1.25  −1.97
FRAP1 FK506 binding protein 12-rapamycin
associated protein 1, mTOR  −1.77  −1.10  +1.92
GYS1 Glycogen synthase 1 (muscle)  +2.14 −1.17  −2.50
GYS2 Glycogen synthase 2 (liver)  −3.18  +1.75 +5.58
IGF1R Insulin-like growth factor 1 receptor  +1.68 −1.21  −2.03
INSR Insulin receptor  +1.59 −1.21  −1.92 1.00 ± 0.07 0.24 ± 0.07 0.30 ± 0.22●
IRS1 Insulin receptor substrate 1  +2.62 −1.60  −4.19 1.01 ± 0.18 0.58 ± 0.05 1.06 ± 0.08●
PIK3CA Phosphoinositide-3-kinase, catalytic, p110  +1.56 −1.19  −1.76
PIK3R1 Phosphoinositide-3-kinase, regulatory 1, p85  +1.55 −1.62  −2.64
PRKCH Protein kinase C, eta  −1.67  +2.00 +3.02
SLC2A4 GLUT4, solute carrier family 2, member 4  +2.58 −1.31  −2.31 1.00 ± 0.06 0.64 ± 0.05 0.87 ± 0.05●
STXBP4 Syntaxin binding protein 4  +1.81 −1.08  −1.96
VAMP2 Synaptobrevin 2  +1.38 −1.38  −1.90
Cell Cycle
BRCA1 Breast cancer 1, early onset  −3.30  +1.79 +5.91
CCNB1 Cyclin B1  −2.97  +2.32 +6.89
CCNB2 Cyclin B2  −2.87  +2.43 +6.97
CCNE1 Cyclin E1  −1.59  +1.44 +2.29
CDC2 Cell division cycle 2, G1 to S and G2 to M  −2.63  +2.38 +6.27
CDK6 Cyclin-dependent kinase 6  −1.70  +1.55 +2.31
CDKN1A Cyclin-dependent kinase inhibitor 1A (p21, Cip1)  −1.60  +2.77 +4.43
CDKN1B Cyclin-dependent kinase inhibitor 1B (p27, Kip1)  +1.31 −1.35  −1.77
CDKN2B Cyclin-dependent kinase inhibitor 2B
(p15, inhibits CDK4)  −2.02  +1.02 +2.06
E2F1 E2F transcription factor 1  −1.28  +1.58 +1.87
E2F6 E2F transcription factor 6  −2.24  +2.08 +4.66
RB1 Retinoblastoma 1 (including osteosarcoma)  −1.57  +1.40 +2.19
SIRT1 Sirtuin  +1.28 −1.37  −1.75
TOP2A Topoisomerase (DNA) II alpha 170 kDa  −2.89  +2.12 +6.12
Metabolism
ACACA ACC1, acetyl-Coenzyme A carboxylase alpha  +1.84 −4.20  −3.32 1.04 ± 0.32 0.04 ± 0.01 0.51 ± 0.10●

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 13
Continued
ACACB ACC2, acetyl-Coenzyme A carboxylase beta  +2.24 +1.04 −2.15
ADIPOQ Adiponectin  +1.15 −1.03  −1.18 1.00 ± 0.120.63 ± 0.15 1.01 ± 0.17
ALDOB Aldolase B, fructose bisphosphate  +2.74 −2.76  −7.57 1.00 ± 0.100.006 ± 0.003 0.016 ± 0.004●
CPT1A Carnitine palmitoyltransferase 1A (liver)  +1.05 +1.49 +1.42
FABP4 Fatty acid binding protein 4  +3.41 −1.19  −4.05 1.00 ± 0.031.21 ± 0.26 1.41 ± 0.29
FASN Fatty acid synthase  +1.14 −1.39  −1.59 1.00 ± 0.020.54 ± 0.13 0.64 ± 0.14 ●
LEP Leptin  −1.17  +1.59 +1.511.05 ± 0.362.84 ± 0.13 1.77 ± 0.15 ●
PEPCK1 PCK1, Phosphoenolpyruvate carboxykinase 1  +4.57 +1.13 −4.69 1.00 ± 0.060.25 ± 0.11 1.46 ± 0.11 ●
SLC27A1 FATP1, fatty acid transporter  +1.76 +1.54 −1.14
UCP2 Uncoupling protein 2  −1.45  +1.79 +2.581.03 ± 0.291.78 ± 0.18 1.49 ± 0.22 ●
Nuclear Receptors
AR Androgen receptor  +1.82 −1.36  −2.48
ESR1 Estrogen receptor 1  +1.43 −1.47  −2.10
NR3C1 Glucocorticoid receptor  +3.97 −1.46  −2.721.02 ± 0.210.60 ± 0.04 0.98 ± 0.29 ●
NCOR1 Nuclear receptor co-repressor 1  +1.82 −1.51  −2.19
THRA Throid hormone receptor alpha  +1.41 −1.47  −2.07
PGC1A PPARγ coactivator 1A  +1.16 −1.37  −1.77
PGC1B PPARγ coactivator 1B  +1.14 −1.70  −1.68
PPARγ Peroxisome proliferator-activated receptor   +1.18 −1.43  −1.68 1.00 ± 0.080.68 ± 0.14 0.80 ± 0.13 ●
Immunity/inflammation
CCL3 Chemokine (C-C motif) ligand 3  −2.49  +2.84 +7.07
CCL13 Chemokine (C-C motif) ligand 13  −2.69  +3.21 +8.63
CERK Ceramide kinase  −1.40  +1.61 +2.25
CXCL3 Chemokine (C-X-C motif) ligand 3  +1.04 +2.68 +2.57
CXCR4 Chemokine (C-X-C motif) ligand 4  −1.32  +1.74 +2.29
FOS v-fos FBJ viral oncogen homolog  −2.13  +1.65 +3.51
IL1R2 Interleukin 1 receptor, type II  −2.74  +1.24 +3.38
IL1RN Interleukin 1 receptor antagonist  −3.49  +9.85 +24.08
SPHK1 Sphingosine kinase 1  −2.25  +1.59 +3.58
FUP: Fat tissues from UP780 treated DIO mice. FV: Fat tissues from high fat diet, HFD, treated DIO mice. FC: Fat tissues from lean control mice.
found in lipid biosynthesis (Figure 1). First, the fatty
acid biosynthesis depends on two major cytoplasmic
enzymes, acetyl-CoA carboxylase (ACC1) and fatty acid
synthase (FASN). Both ACC1 and FASN were decreased
by UP780 (Table 1 and Figure 1). Second, the pentose
phosphate pathway, which produces NADPH for fatty
acid biosynthesis, was also down-regulated by UP780
(Supplement Table 1). Third, fatty acid desaturases
(SCD1 and FADS1/2) and fatty acid elongases (ELOV5/
6) were decreased by UP780, strongly supporting the
mechanism that UP780 decreased liver fatty acid and tri-
glyceride biosyntheses (Table 1 and Figure 1). Free fatty
acid infusion in human induced systemic insulin resis-
tance [26], UP780 could enhance systemic insulin sen-
sitivity by a reduced lipotoxicity, resulting in enhanced
blood glucose control.
Pathway analysis also suggested a cholesterol lower-
ing effect by UP780, by 1) decreasing the rate-limiting
enzyme HMG-CoA reductase (HMGCR) for cholesterol
biosynthesis, 2) increasing the bile acid biosynthesis en-
zymes CYP7A1 and CYP7B1 for increased elimination
of cholesterol through gut, and 3) decreasing apolipo-
protein B for decreased LDL level (Table 1 and Figure
1).

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 14
Figure 1. Liver metabolism modulated by UP780 over high
fat diet. A schematic diagram is constructed to illustrate the
influences exerted by UP780 to the metabolism of carbohy-
drates and lipids in liver.
Increased mitochondrial β-oxidation is a prominent
mechanism of glycemic control [27]. The rate-limiting
enzyme for mitochondrial fatty acid β-oxidation, car-
nitine palmitoyl transferase 1A (CPT1A), was decreased
from HFD-elevated level (2-fold) by UP780 to lean con-
trol level, suggesting decreased β-oxidation. CPT1A ac-
tivity is regulated by the feedback metabolite malonyl-
CoA. Malonyl-CoA concentration in mitochondria de-
pends on the mitochondrial ACC2. ACC2 expression in
UP780 liver was ~3-fold lower than in HFD, suggest-
ing increased β-oxidation (Table 1). The overall activity
of fatty acid β-oxidation in liver might well be increased;
a mechanism that will support a role of UP780 in better
lipid metabolism control but will need further study (Ta-
ble 1 and Figure 1).
Microarray analysis of WAT gene expression offered a
clear explanation for the insulin sensitizing effect by
UP780. Key genes in the insulin receptor signaling path-
way were globally decreased by HFD and globally in-
creased by UP780 (Table 2 and Supplement Figure 6).
Among these key genes, insulin receptor (INSR), IRS-1,
and glucose transporter 4 (GLUT4) were validated by
QPCR (Table 2). With DIO mouse model, HFD feeding
was known to induce insulin resistance [12]. Insulin ac-
tivates INSR tyrosine kinase, which by phosphorylation
of the IRS proteins, transduces insulin signal through
protein kinases to the translocation of GLUTs to plasma
membrane, thereafter increases glucose uptake. This in-
creased glucose uptake from blood in WAT increases the
usage of glucose for lipid biosynthesis and energy stor-
age [28]. Lowered plasma glucose enhances systemic in-
sulin sensitivity. The concerted down-regulation of in-
sulin signaling pathway by HFD and opposing upre- gu-
lation by UP780 strongly pointed to a reversal of in- su-
lin-resistance as an important mechanism underlying the
UP780 normalization of glycemic control and insulin
sensitivity.
Two more categories in WAT gene list were regulated
similarly to the insulin receptor pathway: those involved
in metabolism and nuclear receptor/co-activator/co-rep-
ressor. Again, multiple gene expression variations were
confirmed by QPCR (Table 2). Of note was adiponectin
(ADIPOQ) gene expression, reduced by HFD and re-
stored to control level by UP780 (Table 2 QPCR).
HFD is also known to induce adipose tissue inflamma-
tion and secretion of inflammatory cytokines such as
TNF-α [29]. Many inflammatory genes were among the
highest of up-regulated genes by HFD, with UP780 re-
ducing these gene expressions (Table 2). Similarly, many
genes in the cell cycle pathway were up-regulated by
HFD and decreased by UP780 (Table 2).
3.2. Functional Validation
Quantification at mRNA levels, although powerful in ge-
nerating a global pattern of UP780 mechanism of action,
is limited in depicting protein levels. Western blotting
therefore was used to validate at the protein level for
liver FASN (Figure 2(a), upper). After normalization with
β-actin loading control (Figure 2(a), lower) to lean con-
trol = 1, HFD decreased FASN to 0.7, UP780 further
decreased FASN to 0.5, and GW1929 to 0.6. Therefore
liver FASN protein levels by Western blot correlated to
microarray and QPCR data (Table 1 and Figure 2(a)).
Figure 2. Western blotting for protein ex-
pression levels modified by UP780. (A) Liver
proteins were probed with a mouse mono-
clonal anti-FASN antibody. A fulllength 270
kD FASN and a smaller 60 kD degradation
fragment were reproducible in Western blots.
The blot was re-probed with anti-α-actin anti-
body for protein loading control. (B) WAT Wes-
tern blot was probed for IRS-1 protein levels
and re-probed for α-actin loading control.
Three protein bands 132 kD and up were re-
producibly observed. Positions of molecular
weight markers are either shown in A or mar-
ked in B at the left.

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 15
For WAT, IRS-1 protein level in the insulin signaling
pathway was validated by Western blot (Figure 2(b))
IRS-1 proteins were dramatically decreased by HFD,
much more than the 42% reduction by QPCR (Figure
2(b) and Table 2). UP780 restored some of the IRS-1
proteins (Figure 2(b), upper). Quantification was not
attempted even though β-actin loading control was avail-
able (Figure 2(b), lower) due to background interfer-
ence.
Liver triglyceride and cholesterol levels were meas-
ured from liver lipid extracts to validate the UP780 me-
chanism of action. HFD increased liver triglyceride level
12-fold above lean control. UP780 treatment decreased
liver triglyceride level to 60% of HFD (Figure 3(a)) with
statistical significance of P = 0.029 by T-test. Liver cho-
lesterol levels were not dramatically changed by HFD
over lean control. HFD increased liver cholesterol 25%
over lean control. In correlation to microarray pathway
analysis, UP780 decreased liver cholesterol to 65% of
HFD with statistical significance of P = 0.016 by T-test
(Figure 3(b)).
Morphology of hepatosteatosis was examined (Figure
4). In lean control liver, lipid droplet was not visible.
Vast amount of lipid droplets (black arrowheads) were ob-
served in HFD liver sections. The liver functional unit of
liver parenchyma is centered around the central vein (in-
dicated in Figure 4) with nutrient supply from hepatic
artery and portal vein reaching first to the hepatocytes
distal from the central vein [30]. It was clear from Fig-
ure 4 that in HFD liver more lipid droplets and balloon-
ing were observed in hepatocytes distal from central vein
than proximal. Lipid droplets disappeared almost com-
pletely in the UP780-treated livers. When observed, the
number of lipid droplets per cell in UP780 livers was
much lower than HFD. Lymphocytes (white arrowhead)
0.00
0.05
0.10
0.15
0.20
0.25
0.30
Lean
HFD
UP7 80
GW1929
0
2
4
6
8
10
12
Lean
HFD
UP780
GW1929
Trigly ceride (mg/mg protein)
Cholesterol (g/mg protein)
** **
0.00
0.05
0.10
0.15
0.20
0.25
0.30
Lean
HFD
UP7 80
GW1929
0
2
4
6
8
10
12
Lean
HFD
UP780
GW1929
Trigly ceride (mg/mg protein)
Cholesterol (g/mg protein)
0.00
0.05
0.10
0.15
0.20
0.25
0.30
Lean
HFD
UP7 80
GW1929
0
2
4
6
8
10
12
Lean
HFD
UP780
GW1929
Trigly ceride (mg/mg protein)
Cholesterol (g/mg protein)
** **
(a) (b)
Figure 3. UP780 decreased liver triglyceride and cholesterol
over HFD. Total lipids extracted from liver were used for (a)
triglyceride and (b) cholesterol assays. Liver triglyceride and
liver cholesterol were assayed in replicates and in dilutions, and
independently multiple times. Representative assays were dis-
played. *indicated T-test P value < 0.05 compared to HFD.
Figure 4. Liver steatosis. Formalin-fixed liver thin sec-
tions were stained with hematoxylin-eosin. Liver steatosis
analyses were done for individual animals for each treat-
ment group. Representative photomicrographs were shown.
Black arrowheads, lipid droplets and ballooning. White ar-
rowhead, inflammation. Central vein was indicated on the
HFD liver, and existed in lean control and UP780 liver
sections. Scale bars, 50 μm.
infiltration into liver was observed in HFD liver, not in
lean control liver, and infrequently in UP780 liver (not
shown).
Improvement of insulin sensitivity should be accom-
panied by decreased fasting plasma insulin levels; there-
fore fasting plasma insulin levels were measured for
baseline, week-7 and week-10. In Figure 5, data were
plotted by individual animals within the treatment groups.
Lean control fasting plasma insulin levels were similarly
low at baseline, week-7, and week-10. For HFD, week-7
showed higher fasting plasma insulin levels, but by
week-10, two animals showed decreased fasting plasma
insulin levels. After 18 weeks of high fat feeding, these
two animals probably developed pancreatic islet degen-
eration. GW1929 was as expected. For the UP780 group,
plasma insulin levels were decreased by week-7, and
trended to decrease further at week-10 (Figure 5). Two-
way ANOVA statistical analysis indicated that UP780
significantly decreased fasting plasma insulin compared
to HFD, with P = 0.05, and GW1929 with P = 4.67E-6.
4. DISCUSSION
Microarray pathway analysis and validation indicated the
mechanism of the UP780 effects in increasing insulin
sensitivity and decreasing plasma glucose [18] by de-
creasing liver fatty acid and triglyceride biosynthesis,
increasing liver mitochondria fatty acid α-oxidation (pos-
sibly), and increasing WAT insulin signaling pathway
(therefore increasing insulin sensitivity).
UP780 was discovered by high throughput screening
of differentiated 3T3-L1 adipocytes that identified bo-
tanic substances capable of increasing adiponectin secre-
tio [18]. Adiponectin together with leptin, another adi- n

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 16
Figure 5. Fasting plasma insulin. Plasma insulin levels were plotted by individual animals
per treatment groups of week-0, week-7 and week-10 plasma samples, using SigmaPlot. The
animal numbers indicated were from experimental assignments. The treatment groups of lean
control, HFD, UP780, and GW1929 were indicated in the plots. Each plasma sample was as-
sayed in dilutions and in duplicates, and sometimes in repeats, therefore each data point con-
tained >2 individual measurements. Statistical analysis was by 2-way ANOVA comparing
UP780/GW groups to HFD group, with *indicate P ≤ 0.05 and **indicated P ≤ 0.01.
pokine, in an insulin-resistant lipoatrophic mouse model
completely reversed insulin resistance, but only partially
by adiponectin or leptin alone [31]. In obese and diabetic
rodents and humans, adiponectin levels were decreased,
which were reversed with weight loss and diabetic treat-
ments [31]. Adiponectin, together with adiponectin re-
ceptors AdipoR1 and AdipoR2, sensitizes tissues to in-
sulin through regulation of glucose and fatty acid me-
tabolism, activation of AMP-activated protein kinase
(AMPK), activation of PPARα signaling pathway, and
conversion of the toxic ceramide to beneficial sphin-
gosine through a ceramidase domain in AdipoR1/2 [32,
33]. This UP780 nutrigenomic study was successful in
demonstrating decreased liver fatty acid biosynthesis and
increased WAT insulin sensitivity, in line with adipo-
nectin mechanism. Activation of AMPK by aloe, further-
more, was demonstrated by western blots of AMPK
phosphorylation in WAT of DIO model [34]. Increased
adiponectin gene expression in WAT by UP780 (Table 2)
correlated with its discovery by screening.
Multiple animal/human studies agreed on the hypo-
glycemic effect of aloe [5,13-17,19,35-39] but not the li-
pid-lowering effects. A double-blind, placebo-controll-
ed pilot clinic trial by Devaraj et al. showed significant
cholesterol/LDL reduction by Qmatrix® but not trigly-
ceride, while UP780 caused no change to either blood
triglyceride or cholesterol level [19]. Clinic trial by Hu-
seini et al. claimed that aloe gel reduced both blood cho-
lesterol and triglyceride, but the conclusion should be
dismissed due to faulty statistical data analysis [38]. Cli-
nic trial by Yagi et al. showed reduced blood triglyce-
ride, but not cholesterol, by a high molecular weight fra-
ction of Aloe vera gel. The Yagi study was not blinded
and was without placebo control [39]. The Yongchai-
yudha et al./Bunyapraphatsara et al. clinic studies of Aloe
vera juice also showed reduced blood triglyceride, but
not cholesterol; the studies were single-blinded and pla-
cebo-controlled [36,37].

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 17
In UP780 DIO studies [18], blood triglyceride levels
could be significantly reduced in one experiment but not
another, including the experiment that livers were col-
lected for triglyceride and cholesterol assays (Figure 3)
and for liver steatosis photomicrography (Figure 4).
Such was the variation observed for animal DIO model
where diet was strictly controlled. Fasting blood trigly-
ceride and cholesterol levels are influenced by diet and
additional environmental factors, which is difficult to
control in clinic trials. Compounded with the variations
in aloe preparations and the human genomes, modifica-
tion of Aloe vera gel to blood lipid levels may have too
much variation to be detected reliably. Perhaps, future
clinic studies of Aloe vera gel effect to liver steatosis will
achieve more uniform results.
5. ACKNOWLEDGEMENTS
The authors thank Mr. William Lee, the owner of Unigen, Inc., who
supported the research. The authors thank Dr. Cannon for critical read-
ing of this manuscript. The authors thank Dr. Yuan Zhao, Ms. Julia Foo,
and Ms. Mei Hong for the screening of Unigen plant extract library.
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J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 19
SUPPLEMENTAL MATERIALS
1. MATERIALS AND METHODS
1.1. Tissue Collection from Dio Mouse Model
DIO mice were as described in the companion paper [1].
Lean, HFD, UP780, and GW1929 fasting blood samples
were taken before treatment (baseline), during treatment
(7 weeks), and at the time of euthanasia (10 weeks).
Mice were anesthetized with CO2; liver and visceral
WAT tissues were collected within 5 minutes of euthana-
sia. For RNA isolation, 5 mm tissue strips were preserv-
ed in RNALater (Ambion). For Western blots, triglyce-
ride and cholesterol assays, tissues were snap frozen in
liquid nitrogen and stored at −80˚C. For histology, one
lobe of the livers were fixed in 10% formalin/phosphate
buffered saline (SIGMA) and stored at 4˚C. Fixed livers
were thin sectioned and stained with hematoxylin-eosin
for microscopic observations.
1.2. RNA Extraction
For total RNA extraction, RNEasy kit was used for total
liver RNA extraction, and RNEasy for Fatty Tissue kit
was used for WAT RNA extraction (Qiagen). RNA quail-
ties were determined with glyoxal agarose gel electro-
phoresis (Ambion). When genomic DNA was observed,
a second extraction was carried out.
1.3. Microarray
Affymetrix mouse genome 430 2.0 array was used for
microarray analysis of liver and WAT gene expression.
Microarray procedures followed the standard protocol of
Affymetrix GeneChip one-cycle target preparation [2].
The mouse samples were coded LC, LV, and LUP for
livers of lean-control, HFD, and UP780, respectively,
and FC, FV, and FUP for WAT. Three mice per treatment
group, 3 treatment groups, and 2 tissues, in total 18 mi-
croarray chips were used. All microarray datasets passed
quality controls, including GCOS [3] and Bioconductor
package affy [4] (Supplement Figures 1 and 2). Details
of microarray data analysis followed published proce-
dures [5,6].
1.4. Pathway Analysis
Analysis of microarray data, in the range of 45,000 probe
sets, benefited greatly from the Ingenuity pathway analy-
sis (IPA) software to develop a sense of the biological
significance. The microarray analysis results by Biocon-
ductor of eBayes-adjusted p-values, log2 fold changes,
and log2 expression values were uploaded into the IPA
server. Cutoff criteria of p ≤ 0.05, log2 fold change ≥ 0.8,
and log2 intensity ≥ 3.5 were applied. Furthermore, due
to multiple probe sets per gene minimal p-value was set
to resolve among multiple probe sets. IPA results of ca-
nonical pathways were further analyzed in detail. Infor-
mation of gene functions were from IPA and OMIM da-
tabases [7,8].
1.5. Real-Time QPCR
Total RNAs in excess of the needs for microarray were
LC1.CEL
68101214
-5 05
Median: 0.0144
IQR: 0.329
681012 14
-5 05
Median: -0.0601
IQR: 0.375
LC2 .CEL
681012 14
-5 05
Median: -0.0807
IQR: 0.34LC4.CEL
A
M
MVA
p
l
ot
(a)

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 20
LV1.CEL
6810 1214
-10 -505
Median: 0.0566
IQR: 0.322
681012 14
-10 -505
Median: 0.144
IQR: 0.342
LV2.CEL
681012 14
-10 -50510
Median: 0.0952
IQR: 0.342LV40.CEL
A
M
MVA p lot
(b)
LUP214.CEL
6810 12 14
-505 10
Median: 0
IQR: 0.368
68101214
-505 10
M e dia n: -0 .1 8 6
IQR: 0.346
LUP215.CEL
68101214
-5 05
Median: -0.194
IQ R : 0 .3 2 9LUP25.CEL
A
M
MVA plot
(c)
Supplement Figure 1. Microarray data quality control plots for the nine liver microarray
chips. Probe level data/object (before gcrma, affy preprocessing of background subtrac-
tion, normalization, and summarization of intensities) from the Bioconductor affy pack-
age was used for quality control plots. MVA plots were used for assessing the three bio-
logical replicates each for A. lean control (LC1, LC2, and LC4), B. HFD (LV1, LV2, and
LV40), and C. HFD + UP780 (LUP25, LUP214, and LUP215) chips. The MVA plots of
all pairwise comparisons were particularly useful in diagnosing problems in replicate sets
of arrays. The plots indicated tight correlation among the replicate sets of arrays. Based on
these quality control plots, the nine liver microarray chips were judged to be of good quality.

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 21
FC1.CEL
6810 12 14
-10 -50510
Median: 0.125
IQR: 0.323
68101214
-505 10
Median: 0.117
IQR: 0.390
FC2.CEL
6810 12 14
-50510
Median: 0
IQR: 0 .4 3 1FC4.CEL
A
M
MVA pl o t
(a)
FV1.CEL
6810 12 14
-10 -50510
Median: 0.173
IQR: 0.559
6810 1214
-10 -50510
Median: 0.189
IQR: 0.523
FV2.CEL
681012 14
-10 -50510
Median: 0.00394
IQR : 0 .34 4FV40.CEL
A
M
MVA pl o t
(b)

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 22
(c)
Supplement Figure 2. Microarray data quality control plots for the nine WAT microarray
chips. Probe level data/object from affy package (before gcrma preprocessing of back-
ground subtraction, normalization, and summarization of intensities), the Bioconductor affy
package was used for quality control plots. MVA plots were used for assessing the three
biological replicates each for A. lean control (FC1, FC2, and FC4), B. HFD (FV1, FV2,
and FV40), and C. HFD + UP780 (FUP25, FUP214, and FUP215) chips. The MVA plots of
all pairwise comparisons were particularly useful in diagnosing problems in replicate sets
of arrays. The plots indicated tight correlation among the replicate sets of arrays. Based on
these quality control plots, the nine WAT microarray chips were judged to be of good qual-
ity.
combined for QPCR. Superscript III reverse transcriptase
(Invitrogen) was used for cDNA synthesis. The ABI
TaqMan Gene Expression assays for the selected genes
were confirmed by RefSeq accession numbers before use,
to ensure the sequences used by the Affymetrix mouse
genome 430 2.0 array and the ABI TaqMan Gene Ex-
pression assays were compatible. Thermal cycling and
fluorescence detection was performed by an ABI 7700
Sequence Detector. The relative quantification method of
ΔΔCT was used for data analysis. Most QPCR runs were
multiplex reactions and each plate contained at least one
control cDNA (the lean control) and each well contained
the GAPDH internal control. Singleplex QPCR was used
for abundant transcripts such as adiponectin with GAPDH
controls in separate wells. QPCR reactions were
run in triplicates and results expressed as mean ± S.D.
1.6. Western Blot
Mouse liver and WAT were homogenized in RIPA buffer
(50 mM Tris.HCl pH 7.4, 150 mM NaCl, 1% Triton
X-100, 0.25% deoxycholate, supplemented with a prote-
ase inhibitor cocktail (Roche) and a phosphatase inhibi-
tor cocktail (Pierce)) and debris removed by centrifuga-
tion at 5000 g for 5 min. Protein concentrations were
determined by BCA protein assay (Pierce). Twenty five
μg of liver proteins and 50 μg of WAT proteins were used
per lane for 4% - 12% Bis-Tris gel electrophoresis (Invi-
trogen). The proteins were electroporated onto PVDF

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 23
membranes and immunoblotted: mouse monoclonal an-
tibody specific for fatty acid synthase (FASN) at 1:1000
dilution, rabbit polyclonal antibody specific for insulin
receptor substrate-1 (IRS-1) at 1:200 dilution, and secon-
dary HRP-conjugated antibodies at 1:3000 dilution for anti-
mouse IgG and 1:5000 dilution for anti-rabbit IgG (Santa
Cruz); detected with ECL-Plus chemiluminescence solu-
tion and ECL film (GE Healthcare). For quantification,
ECL films were scanned and the band intensities analy-
zed with NIH ImageJ software.
1.7. Liver Triglyceride and Cholesterol Assays
Liver homogenates and protein BCA assay were as de-
scribed for Western blot. Liver homogenates were mixed
with two volumes of methanol and chloroform (1:3, by
volume) and shook vigorously for 10 minutes, then cen-
trifuged for 15 minutes at 14,000 rpm. The organic layers
were transferred to clean tubes. Extraction was repeated
and the two organic fractions combined. The organic frac-
tions were dried under N2 gas, then resuspended in eth-
anol. The extracted lipids were assayed in duplicate us-
ing triglyceride assay kits (Cayman Chemicals and Sig-
ma-Aldrich) and a cholesterol assay kit (Cayman Che-
micals). Each assay plate included a standard curve (Cay-
man Chemicals). Several dilutions for each sample were
tested. The total liver triglyceride and cholesterol con-
centrations were normalized by protein concentrations in
the initial liver homogenates, and expressed as mean ±
S.D. Statistical analysis used T-test.
1.8. Insulin ELISA Assay
Plasma samples collected at baseline, week-7 and week-
10 of treatments were used for mouse insulin ELISA
(Crystal Chem). A standard curve was included in every
assay plate and all samples were assayed in duplicates.
For assay results that fell outside the range of the stan-
dard curves, ELISA assays were repeated with dilutions.
SigmaPlot was used for standard curve-fitting (logistic
4-parameter) and X-Y conversion. Results were express-
ed as mean ± S.D. Statistical analysis used 2-way ANOVA
(SigmaStat).
2. RESULTS AND DISCUSSIONS
2.1. Microarray Data Analysis
The nine-chip datasets from tissue samples (liver or WAT)
were read-in together using the Bioconductor affy pack-
age [5] as one object, so that the subsequent preprocess-
ing steps could be conducted as one experiment. The pre-
processing steps of background correction, normalization,
and summarization of the expression values were carried
out using the gcrma package, taking advantage of the
background adjustment feature with probe GC-content
sequence information [9]. The expression values gene-
rated by gcrma were summarized as log2 transformed
expression values. Statistical analyses for differential ex-
pressions by Student’s T-test were calculated by using the
linear model as implemented in the limma package [6].
Three contrasts, HFD + UP780 vs. HFD, HFD + UP780
vs. lean control, and HFD vs. lean control, were compu-
ted using the lmfit function, followed by the eBayes func-
tion to adjust the standard errors of the log2-fold changes
for the 3 contrasts, or false discovery rate (FDR) [6]. The
analysis results of adjusted p-values, log2 fold changes,
and log2 expression values were uploaded to the Inge-
nuity IPA [8] website for pathway analysis.
Global views of gene expression variations influenced
by HFD and by UP780 on top of HFD were extracted
from the results of limma linear model fits [6]. In Sup-
plement Figures 3(a) and (b), Venn diagrams show the
number of significant gene expression variations scored
by limma and the number of overlapping genes shared by
the comparisons between lean control (LC and FC), HFD
(LV and FV), and HFD+UP780 (LUP and FUP). The dis-
tributions of up- or down-regulations are plotted in Sup-
plement Figure 3(c) for liver and Supplement Figure
3(d) for WAT. Among the 729 LUP-LC significant genes,
425 were up-regulated and 304 were down regulated.
Among the 661 LV-LC significant genes, 486 were up-
regulated and 175 were down regulated (Supplement Fig-
ure 3(c)). Apparently in liver, HFD tends to induce gene
expression levels and UP780 tends to reduce gene ex-
pression levels. This trend became clear when indivi-
dual genes in significant metabolic and signaling path-
ways were examined (Table 1 and Supplement Tables 1
and 2).
From WAT far more genes were scored significant,
and had larger fold-changes as compared to liver (Sup-
plement Figure 3(c) and (d)). Among the 660 FUP-FC
significant genes, 278 were up-regulated and 382 were
down-regulated. Among the 2705 significant FV-FC genes,
1025 were up-regulated and 1680 were down-regulated
(Supplement Figure 3(d)). The large gene number dif-
ference between FUP-FC and FV-FC suggested that in
WAT, HFD caused wide-spread and strong gene expres-
sion regulations, and UP780 treatment decreased glob-
ally these gene expression regulations to be closer to the
lean control.
2.2. IPA Pathway Analysis
The pathways were ranked by right-tailed Fisher’s exact
test for the significance of changes between two con-
trasts, taken into consideration 1) the number of genes
that passed the cutoff and were also in the pathway, 2)

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 24
(a) (b)
Gene Index
010000 20000 30000 40000
Log2 Fold-Change
-4
-2
0
2
4
6
LV-LC
LUP-LC
LC-LC
(c)
Gene Index
010000 20000 30000 40000
Log2 Fold-Change
-6
-4
-2
0
2
4
6
8
FV-FC
FUP-FC
FC-FC
(b)
Supplement Figure 3. Gene Expression variations by linear model fit. Significant gene expression varia-
tions were data exported from limma linear model fit. Venn diagrams show the numbers of genes with dif-
ferential expression from the three comparisons and the gene numbers of overlapping distribution be-
tween and among the three comparisons, A liver, B WAT. The differentially expressed genes in individual
comparisons of Venn diagrams were plotted to show the distribution of up- or down-regulated genes in-
fluenced by HFD and by HFD + UP780, using the lean controls as the baseline, C liver, D WAT. Gene in-
dex was numbered according to the gene-ID list of the Affymetrix mouse genome 430.2 chip.

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 25
Supplement Table 1.
LUP/LV LUP/LC LV/LC
Name Description RefSeq ID
p-value Log2
Ratio Intensity p-valueLog2 Ratio Intensity p-value Log2 Ratio Intensity
Pyruvate Metabolism
ACACB acetyl-Coenzyme A
carboxylase beta NM_133904 0.01 −1.6415.459 0.015−1.4986.957 0.762 0.1437.1
ACAT2 acetyl-Coenzyme A
acetyltransferase 2 NM_009338 0.035−0.58610.9350.005 −0.92711.862 0.117 0.15212.068
ACSL3
acyl-CoA
synthetase long-chain
family member 3
NM_0010336060.011 −0.8257.664 0.064−0.5198.184 0.233 0.3058.489
ACSS2
acyl-CoA synthetase
short-chain
family member 2
NM_019811 0.313−0.52911.2180.02 −1.49912.717 0.054 −1.0311.548
ACYP1
acylphosphatase 1,
erythrocyte
(common) type
NM_025421 0.0041.2147.721 0.0130.9376.784 0.234 −0.3867.339
AKR1B1
aldo-keto reductase
family 1, member B1
(aldose reductase)
NM_009658 0.0020.8527.936 0.0260.4727.464 0.018 −0.5875.291
ALDH1B1 aldehyde dehydrogenase
1 family, member B1 NM_028270 0.008−1.6066.814 0.094−0.8277.641 0.111 0.7798.419
ALDH3A2 aldehyde dehydrogenase
3 family, member A2 NM_007437 0.048−0.65411.2960.5160.18411.112 0.019
0.838 11.949
ALDH5A1
aldehyde dehydrogenase
5 family, member A1
(succinate-semialdehyde
dehydrogenase)
NM_172532 0.008−0.8088.158 0.09 −0.4228.58 0.114 0.3878.966
DLAT dihydrolipoamide
S-acetyltransferase NM_145614 0.003−0.8958.757 0.003−0.9039.66 0.803 0.0847.625
ME1
malic enzyme 1,
NADP(+)-dependent,
cytosolic
NM_008615 0.012−1.13711.44 0.017−1.05812.499 0.7 −0.17211.28
NUDT7
nudix (nucleoside
diphosphate linked
moiety X)-type motif 7
NM_024437 0.0011.08314.423 0.0280.56513.857 0.039 −0.51813.34
PC pyruvate carboxylase NM_008797 0.011−0.63211.0290.0430.45 10.579 0.001
1.08111.66
PKLR pyruvate kinase, liver
and RBC NM_0010997790.006 −1.1799.396 0.142−0.6268.63 0.049 0.7 10.574
Glycolysis/Gluconeogenesis
ACSL3
acyl-CoA synthetase
long-chain family
member 3
NM_0010336060.011 −0.8257.664 0.064−0.5198.184 0.233 0.3058.489
ACSS2
acyl-CoA synthetase
short-chain family
member 2
NM_019811 0.313−0.52911.2180.02 −1.49912.717 0.054 −1.0311.548
ACYP1
acylphosphatase 1,
erythrocyte (common)
type
NM_025421 0.0041.2147.721 0.0130.9376.784 0.234 −0.3867.339
ALDH1B1 aldehyde dehydrogenase
1 family, member B1 NM_028270 0.008−1.6066.814 0.094−0.8277.641 0.111 0.7798.419
ALDH3A2 aldehyde dehydrogenase
3 family, member A2 NM_007437 0.048−0.65411.2960.5160.18411.112 0.019
0.838 11.949
ALDH5A1
aldehyde dehydrogenase
5 family, member A1
(succinate-semialdehyde
dehydrogenase)
NM_172532 0.008−0.8088.158 0.09 −0.4228.58 0.114 0.3878.966
ALDOC aldolase C, fructose-
bisphosphate NM_009657 0.5440.2148.518 0.066−0.7449.262 0.027
−0.9588.304
BPGM 2,3-bisphosphoglycerate
mutase NM_007563 0.004−1.097.804 0.001−1.6329.436 0.072 −0.5428.894
DLAT dihydrolipoamide
S-acetyltransferase NM_145614 0.003−0.8958.757 0.003−0.9039.66 0.803 0.0847.625
G6PC glucose-6-phosphatase,
catalytic subunit NM_008061 0.098−0.64112.013 0.6410.16111.851 0.049
0.803 12.654

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 26
Continued
GCK glucokinase (hexokinase 4) NM_010292 0.008−1.1938.679 0.5110.182 8.288 0.007 1.03 9.318
GPI glucose phosphate isomerase NM_008155 0.001−0.8511.57 0.224−0.209 11.779 0.005 0.64212.42
HK1 hexokinase 1 NM_010438 0 −1.3483.313 0.006−0.826 4.139 0.015 −0.475 12.23
PFKL phosphofructokinase, liver NM_008826 0.024−0.7348.904 0.2050.363 7.152 0.006
1.005 9.638
PGM1 phosphoglucomutase 1 NM_025700 0.003−0.889 10.7290.142−0.326 11.054 0.026 0.564 11.618
PGM3 phosphoglucomutase 3 NM_028352 0.271−0.3816.948 0.0380.827 6.122 0.008 1.208 7.329
PKLR pyruvate kinase, liver
and RBC NM_0010997790.006 −1.1799.396 0.142−0.626 8.63 0.049 0.7 10.574
Fatty Acid Biosynthesis
ACACB acetyl-Coenzyme A
carboxylase beta NM_133904 0.01
−1.6415.459 0.015−1.498 6.957 0.762 0.1437.1
ACSL3
acyl-CoA synthetase
long-chain
family member 3
NM_0010336060.011 −0.8257.664 0.064−0.519 8.184 0.233 0.305 8.489
FASN fatty acid synthase NM_007988 0.002−1.961 11.0540.012−1.338 12.392 0.154 0.623 13.015
Androgen/Estrogen Metabolism
ARSA arylsulfatase A NM_009713 0.038−0.8058.473 0.053−0.735 9.208 0.827 0.079.279
ARSB arylsulfatase B NM_009712 0.006−1.0327.29 0.073−0.555 7.845 0.112 0.477 8.322
ARSG arylsulfatase G NM_028710 0.908−0.0198.523 0 1.165 7.359 0 1.184 8.542
CYP7B1 cytochrome P450, family 7,
subfamily B, polypeptide 1 NM_007825 0.0051.46412.8380.0131.203 11.635 0.404 −0.286 12.756
HSD17B4 hydroxysteroid (17-beta)
dehydrogenase 4 NM_008292 0.007−0.6612.3080.41 0.149 12.159 0.003
0.809 12.968
HSD17B7 hydroxysteroid (17-beta)
dehydrogenase 7 NM_010476 0.041−0.6687.674 0.018−0.827 8.501 0.555 −0.152 10.318
STS steroid sulfatase
(microsomal), isozyme S NM_009293 0.016−0.9957.962 0.175−0.466 8.428 0.13 0.538.957
SULF2 sulfatase 2 NM_028072 0.023−1.1783.59 0.126−0.497 6.836 0.058 0.912 4.768
UGT2B10 UDP glucuronosyltransferase
2 family, polypeptide B10 NM_053215 0.0241.634.538 0.1041.041 3.497 0.322 −0.5892.908
UGT2B17 UDP glucuronosyltransferase
2 family, polypeptide B17 NM_133894 0.0073.3888.373 0.1071.639 6.734 0.075 −0.247 13.76
Pentose Phosphate Shunt
ALDOC aldolase C, fructose-
bisphosphate NM_009657 0.5440.2148.518 0.066−0.744 9.262 0.027
−0.958 8.304
GPI glucose phosphate isomerase NM_008155 0.001−0.8511.57 0.224−0.209 11.779 0.005 0.64212.42
PFKL phosphofructokinase, liver NM_008826 0.024−0.7348.904 0.2050.363 7.152 0.006 1.005 9.638
PGD phosphogluconate
dehydrogenase NM_0010812740.026−1.1817.348 0.114−0.745 8.093 0.147 0.5498.851
PGM1 phosphoglucomutase 1 NM_025700 0.003−0.889 10.7290.142−0.326 11.054 0.026 0.564 11.618
PGM3 phosphoglucomutase 3 NM_028352 0.271−0.3816.948 0.0380.827 6.122 0.008 1.208 7.329
RPIA
ribose 5-phosphate
isomerase A (ribose
5-phosphate epimerase)
NM_009075 0.004−1.0745.833 0.045 −0.6 6.433 0.094 0.4746.907
TKT
transketolase
(Wernicke-Korsakoff
syndrome)
NM_009388 0.001−1.358.781 0.012−0.852 9.633 0.06 0.53711.842
Glycerophospholipid Metabolism
AGPAT3 1-acylglycerol-3-phosphate
O-acyltransferase 3 NM_053014 0.004−1.8097.367 0.159−0.655 8.022 0.005 0.63310.017
CHKA choline kinase alpha NM_0010255660.036−0.5782.754 0.2980.287 7.425 0.017 0.812 8.237

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 27
Continued
GPAM
glycerol-3-phosphate
acyltransferase,
mitochondrial
NM_0081490.013 −1.21311.8020.05−0.862 12.663 0.36 0.35113.015
GPD1 glycerol-3-phosphate
dehydrogenase 1 (soluble) NM_0102710.003 −0.861 10.337 0.258 −0.227 10.565 0.012 0.63411.199
GPD2
glycerol-3-phosphate
dehydrogenase 2
(mitochondrial)
NM_0102740.004 −0.8718.9680.254 −0.011 2.295 0.002 0.989 9.839
GRN granulin NM_0081750.014−0.862 10.889 0.094 −0.501 11.391 0.11 0.49310.695
LIPG lipase, endothelial NM_0107200.075−0.7183.6940.1930.422 5.104 0.012
1.016 6.12
MGLL monoglyceride lipase NM_0118440.003−0.80111.2440.1120.317 10.927 0.001 1.118 12.045
PCYT1A phosphate cytidylyltransferase
1, choline, alpha NM_0099810.001 −1.3236.7180.007 −0.806 7.524 0.043 0.5178.041
PIGF phosphatidylinositol glycan
anchor biosynthesis, class F NM_008838 0.001 1.213 7.7980.0110.726 7.072 0.052 −0.488 6.585
PLA2G4A phospholipase A2, group IVA
(cytosolic, calcium-dependent) NM_008869 0.004 1.1115.765 0.0130.879 4.886 0.396 −0.232 4.654
PPAP2B phosphatidic acid
phosphatase type 2B NM_0805550.014 −0.831 10.244 0.057 −0.573 10.817 0.305 0.18111.441
Xenobiotic Metabolism by P450
CYP1A2 cytochrome P450, family 1,
subfamily A, polypeptide 2 NM_0099930.0690.39912.721 0.003 −0.847 13.568 0 −1.246 12.323
CYP2A13 cytochrome P450, family 2,
subfamily A, polypeptide 13 NM_0078120.503 −0.321 11.5040.02−1.399 12.903 0.052 −1.078 11.825
CYP2B6
(includes EG:1555)
cytochrome P450, family 2,
subfamily B, polypeptide 6 NM_0099980.026 −0.9482.4340.002 −1.753 4.175 0.044 −0.546 2.408
CYP2B9 cytochrome P450, family 2,
subfamily b, polypeptide 9 NM_0100000.001 −5.3222.8960.684 −0.354 3.249 0.001 4.969 8.218
CYP2C38 cytochrome P450, family 2,
subfamily c, polypeptide 38 NM_0100020.001 −2.0337.6490.015 −1.247 8.896 0.079 0.7869.682
CYP2C54 cytochrome P450, family 2,
subfamily c, polypeptide 54 NM_2065370.0190.49413.689 0.088−0.32 14.01 0.002
−0.815 13.195
CYP2C55 cytochrome P450, family 2,
subfamily c, polypeptide 55 NM_0280890.4790.2146.4310 −1.945 8.376 0 −2.158 6.217
CYP2D13 cytochrome P450, family 2,
subfamily d, polypeptide 13 NR_0035520.005 0.973 6.4270.0440.582 5.845 0.141 −0.391 5.454
CYP2G1P
cytochrome P450, family
2, subfamily G, polypeptide
1 pseudogene
NM_013809 0.874 0.0373.222 0.002−1.19 4.411 0.001 −1.227 3.185
GSTA4 glutathione S-transferase A4 NM_0103570.4170.14910.430.003−0.779 11.209 0.001 -0.928 10.281
GSTA5 glutathione S-transferase A5 NM_0081810.133−1.0137.6340.001 −2.393 10.925 0.004 −1.8 9.126
GSTM1
(includes EG:14862) glutathione S-transferase, mu 1 NM_0103580 −0.8613.6650 −1.256 7.021 0.016 −0.409 6.612
GSTM1
(includes EG:2944) glutathione S-transferase M1 NM_0081830.001−0.9978.9650 −1.162 10.127 0.332 −0.1659.962
GSTM3
(includes EG:14864) glutathione S-transferase, mu 3 NM_0103590.016−1.4169.9390.001 −2.399 12.338 0.061 −0.98211.356
GSTM4 glutathione S-transferase M4 NM_0267640.097−0.4699.2310.002 −1.226 10.456 0.019 −0.757 9.699
GSTM5 glutathione S-transferase M5 NM_0081840.376−0.14910.351 0.002 −0.818 11.169 0.005 −0.66910.501
GSTT3 glutathione S-transferase,
theta 3 NM_1339940.002 −1.0728.570.001−1.275 9.845 0.366 −0.203 9.642
MGST3 microsomal glutathione
S-transferase 3 NM_0255690.131 −0.4597.7260.009 −0.982 8.708 0.093 −0.523 8.185
UGT2B10 UDP glucuronosyltransferase
2 family, polypeptide B10 NM_053215 0.0241.634.538 0.104 1.041 3.497 0.322 −0.589 2.908
UGT2B17 UDP glucuronosyltransferase
2 family, polypeptide B17 NM_133894 0.007 3.3888.373 0.107 1.639 6.734 0.075 −0.247 13.76
Fatty Acid Metabolism
ACAA1B acetyl-Coenzyme A
acyltransferase 1B NM_1308640.002 −0.91212.809 0.048 −0.279 14.769 0.027 0.44114.5

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 28
Continued
ACAD11
acyl-Coenzyme A
dehydrogenase
family, member 11
NM_028721 0.018−0.54212.110.1740.262 11.847 0.003 0.80412.651
ACAT2 acetyl-Coenzyme A
acetyltransferase 2 NM_009338 0.035−0.58610.935 0.005 −0.927 11.862 0.117 0.15212.068
ACOX1 acyl-Coenzyme A oxidase
1, palmitoyl NM_015729 0.002−0.90113.030.298−0.207 13.236 0.008 0.69413.93
ACSL3 acyl-CoA synthetase
long-chain family member 3 NM_0010336060.011 −0.8257.6640.064 −0.519 8.184 0.233 0.3058.489
ALDH1B1 aldehyde dehydrogenase
1 family, member B1 NM_028270 0.008−1.6066.8140.094 −0.827 7.641 0.111 0.7798.419
ALDH3A2 aldehyde dehydrogenase
3 family, member A2 NM_007437 0.048−0.65411.2960.5160.184 11.112 0.019 0.838 11.949
ALDH5A1
aldehyde dehydrogenase
5 family, member A1
(succinate-semialdehyde
dehydrogenase)
NM_172532 0.008−0.808 8.1580.09 −0.422 8.58 0.114 0.387 8.966
CPT1A carnitine palmitoyltransferase
1A (liver) NM_013495 0.008−0.83411.1370.2520.279 10.858 0.002 1.11411.972
CYP1A2 cytochrome P450, family 1,
subfamily A, polypeptide 2 NM_009993 0.0690.39912.7210.003−0.847 13.568 0 −1.246 12.323
CYP2A13 cytochrome P450, family 2,
subfamily A, polypeptide 13 NM_007812 0.503−0.321 11.5040.02−1.399 12.903 0.052 −1.078 11.825
CYP2B6
(includes EG:1555)
cytochrome P450, family 2,
subfamily B, polypeptide 6 NM_009998 0.026−0.9482.4340.002 −1.753 4.175 0.044 −0.546 2.408
CYP2B9 cytochrome P450, family 2,
subfamily b, polypeptide 9 NM_010000 0.001−5.3222.8960.684 −0.354 3.249 0.001 4.969 8.218
CYP2C38 cytochrome P450, family 2,
subfamily c, polypeptide 38 NM_010002 0.001−2.0337.6490.015 −1.247 8.896 0.079 0.7869.682
CYP2C54 cytochrome P450, family 2,
subfamily c, polypeptide 54 NM_206537 0.0190.49413.6890.088−0.32 14.01 0.002
−0.815 13.195
CYP2C55 cytochrome P450, family 2,
subfamily c, polypeptide 55 NM_028089 0.4790.2146.431 0
−1.945 8.376 0 −2.158 6.217
CYP2D13 cytochrome P450, family 2,
subfamily d, polypeptide 13 NR_003552 0.0050.973 6.4270.0440.582 5.845 0.141 −0.391 5.454
CYP2G1P
cytochrome P450, family 2,
subfamily G, polypeptide 1
pseudogene
NM_013809 0.8740.0373.2220.002−1.19 4.411 0.001 −1.227 3.185
CYP4A14 cytochrome P450, family 4,
subfamily a, polypeptide 14 NM_007822 0.04−1.50611.520.364 −0.571 12.091 0.159 0.934 13.026
HSD17B4 hydroxysteroid (17-beta)
dehydrogenase 4 NM_008292 0.007−0.6612.3080.410.149 12.159 0.003 0.80912.968
Bile Acid Biosynthesis
ACAA1B acetyl-Coenzyme A
acyltransferase 1B NM_130864 0.002−0.91212.809 0.048 −0.279 14.769 0.027 0.44114.5
ALDH1B1 aldehyde dehydrogenase 1
family, member B1 NM_028270 0.008−1.6066.8140.094 −0.827 7.641 0.111 0.7798.419
ALDH3A2 aldehyde dehydrogenase 3
family, member A2 NM_007437 0.048−0.65411.2960.5160.184 11.112 0.019 0.83811.949
ALDH5A1
aldehyde dehydrogenase 5
family, member A1
(succinate-semialdehyde
dehydrogenase)
NM_172532 0.008−0.808 8.1580.09 −0.422 8.58 0.114 0.387 8.966
CYP7A1 cytochrome P450, family 7,
subfamily A, polypeptide 1 NM_007824 0.0641.4729.6350.082 −1.292 7.267 0.012 −2.291 8.163
CYP7B1 cytochrome P450, family 7,
subfamily B, polypeptide 1 NM_007825 0.0051.46412.838 0.0131.203 11.635 0.404 −0.28612.756
Glycerolipid Metabolism
AGPAT3 1-acylglycerol-3-phosphate
O-acyltransferase 3 NM_053014 0.004−1.8097.3670.159 −0.655 8.022 0.005 0.633 10.017
AKR1B1 aldo-keto reductase family 1,
member B1 (aldose reductase) NM_009658 0.0020.852 7.9360.0260.472 7.464 0.018 −0.587 5.291
ALDH1B1 aldehyde dehydrogenase
1 family, member B1 NM_028270 0.008−1.6066.8140.094 −0.827 7.641 0.111 0.7798.419
ALDH3A2 aldehyde dehydrogenase
3 family, member A2 NM_007437 0.048−0.65411.2960.5160.184 11.112 0.019 0.838 11.949

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 29
Continued
ALDH5A1
aldehyde dehydrogenase
5 family, member A1
(succinate-semialdehyde
dehydrogenase)
NM_172532 0.008−0.808 8.1580.09−0.422 8.58 0.114 0.387 8.966
GPAM
glycerol-3-phosphate
acyltransferase,
mitochondrial
NM_008149 0.013−1.213 11.8020.05−0.862 12.663 0.36 0.35113.015
LIPG lipase, endothelial NM_010720 0.075−0.7183.6940.1930.422 5.104 0.012 1.016 6.12
MGLL monoglyceride lipase NM_011844 0.003−0.80111.2440.1120.317 10.927 0.001 1.118 12.045
MOGAT1 monoacylglycerol
O-acyltransferase 1 NM_026713 0.074−1.1783.0380.6540.259 2.779 0.038 1.438 4.217
PPAP2B phosphatidic acid
phosphatase type 2B NM_080555 0.014−0.831 10.244 0.057 −0.573 10.817 0.305 0.18111.441
Aminosugar Metabolism
CYB561 cytochrome b-561 NM_007805 0.036−0.6665.1220.2720.303 4.819 0.008 0.969 5.788
CYB5R3 cytochrome b5 reductase 3 NM_029787 0.009−0.809 11.9750.03−0.605 12.58 0.231 0.23513.42
GCK glucokinase (hexokinase 4) NM_010292 0.008−1.1938.6790.5110.182 8.288 0.007 1.03 9.318
GFPT1
glutamine-fructose-6-
phosphate
transaminase 1
NM_013528 0.024−0.8096.7240.2720.001 2.286 0.044 0.1692.533
HK1 hexokinase 1 NM_010438 0
−1.3483.3130.006 −0.826 4.139 0.015 −0.47512.23
NQO1 NAD(P)H dehydrogenase,
quinone 1 NM_008706 0.064−0.8833.7050.035 −1.056 4.761 0.677 −0.172 4.589
PDE2A phosphodiesterase 2A,
cGMP-stimulated NM_0010085480.001 −1.4264.7730.002 −1.319 6.092 0.653 0.1169.205
PDE4B
phosphodiesterase 4B,
cAMP-specific
(phosphodiesterase E4
dunce homolog, Drosophila)
NM_019840 0.004−0.9672.6810.254 −0.007 2.321 0.009 0.8083.647
PDE7B phosphodiesterase 7B NM_013875 0.002−0.826 5.3050.07 −0.349 5.655 0.023 0.4766.131
PGM3 phosphoglucomutase 3 NM_028352 0.271−0.381 6.9480.038 0.827 6.122 0.008 1.208 7.329
Sphingolipid Metabolism
ARSA arylsulfatase A NM_009713 0.038−0.8058.4730.053 −0.735 9.208 0.827 0.079.279
ARSB arylsulfatase B NM_009712 0.006−1.0327.290.073 −0.555 7.845 0.112 0.4778.322
ARSG arylsulfatase G NM_028710 0.908−0.0198.5230 1.165 7.359 0 1.184 8.542
CYP26A1 cytochrome P450, family 26,
subfamily A, polypeptide 1 NM_007811 0.022−1.991 5.192 0.001 −3.72 8.911 0.037 −1.729 7.183
PPAP2B phosphatidic acid
phosphatase type 2B NM_080555 0.014−0.831 10.244 0.057 −0.573 10.817 0.305 0.18111.441
SULF2 sulfatase 2 NM_028072 0.023−1.1783.590.126 −0.497 6.836 0.058 0.912 4.768
VNN1 vanin 1 NM_011704 0.059−0.8829.3650.0860.764 10.887 0.004 1.658 10.247
Glutathione Metabolism
ACSS2
acyl-CoA synthetase
short-chain
family member 2
NM_019811 0.313−0.529 11.2180.02−1.499 12.717 0.054 −1.03 11.548
GSTA4 glutathione S-transferase A4 NM_010357 0.4170.14910.430.003−0.779 11.209 0.001 −0.928 10.281
GSTA5 glutathione S-transferase A5 NM_008181 0.133−1.0137.6340.001 −2.393 10.925 0.004 −1.8 9.126
GSTM1
(includes EG:14862) glutathione S-transferase, mu 1 NM_010358 0 −0.8613.6650 −1.256 7.021 0.016 −0.4096.612
GSTM1
(includes EG:2944) glutathione S-transferase M1 NM_008183 0.001−0.9978.9650 −1.162 10.127 0.332 −0.165 9.962
GSTM3
(includes EG:14864) glutathione S-transferase, mu 3 NM_010359 0.016−1.4169.9390.001 −2.399 12.338 0.061 −0.982 11.356

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 30
Continued
GSTM4 glutathione S-transferase M4 NM_026764 0.097−0.4699.2310.002−1.226 10.456 0.019 −0.757 9.699
GSTM5 glutathione S-transferase M5 NM_008184 0.376−0.149 10.3510.002 −0.818 11.169 0.005 −0.669 10.501
GSTT3 glutathione S-transferase,
theta 3 NM_133994 0.002−1.0728.570.001 −1.275 9.845 0.366 −0.2039.642
MGST3 microsomal glutathione
S-transferase 3 NM_025569 0.131−0.4597.7260.009 −0.982 8.708 0.093 −0.5238.185
PGD phosphogluconate
dehydrogenase NM_0010812740.026 −1.1817.3480.114−0.745 8.093 0.147 0.5498.851
Biosynthesis of Steroid
CYP26A1 cytochrome P450, family 26,
subfamily A, polypeptide 1 NM_138656 0.022−1.9915.192 0.001 −3.72 8.911 0.037 −1.7297.183
CYP7B1 cytochrome P450, family 7,
subfamily B, polypeptide 1 NM_007811 0.0051.46412.8380.0131.203 11.635 0.404 −0.286 12.756
DHCR7 7-dehydrocholesterol
reductase NM_146006 0.085−0.6769.6890.022−1.006 10.694 0.289 0 2.285
FDPS
farnesyl diphosphate
synthase (farnesyl
pyrophosphate synthetase,
dimethylallyltranstransferase,
geranyltranstransferase)
NM_007825 0.072−0.476 11.3310.004 −0.996 12.327 0.055 −0.52 11.807
HMGCR 3-hydroxy-3-methylglutaryl-
Coenzyme A reductase NM_134469 0.428−0.2546.790.007 −1.179 7.969 0.02 −0.925 7.044
IDI1 isopentenyl-diphosphate
delta isomerase 1 NM_008706 0.140.56110.5190.226−0.446 10.965 0.022 −1.0079.958
LSS
lanosterol synthase
(2,3-oxidosqualene-
lanosterol cyclase)
NM_145360 0.4120.042.4690.023−1.037 6.498 0.04 −0.889 5.609
MVD mevalonate (diphospho)
decarboxylase NM_008255 0.005−1.4316.1810.008 −1.329 7.51 0.776 0.102 7.613
NQO1 NAD(P)H dehydrogenase,
quinone 1 NM_026784 0.064−0.8833.7050.035−1.056 4.761 0.677 −0.1724.589
PMVK phosphomevalonate kinase NM_007856 0.9410.0268.5980.041−0.87 9.467 0.037 −0.896 8.571
Tryptophan Metabolism
ACAT2 acetyl-Coenzyme A
acetyltransferase 2 NM_009338 0.035−0.586 10.9350.005 −0.927 11.862 0.117 0.15212.068
AFMID arylformamidase NM_027827 0.0080.5276.5360.001−0.78 8.825 0 −1.084 6.009
ALDH1B1 aldehyde dehydrogenase 1
family, member B1 NM_028270 0.008−1.6066.8140.094−0.827 7.641 0.111 0.7798.419
ALDH3A2 aldehyde dehydrogenase 3
family, member A2 NM_007437 0.048−0.65411.2960.5160.184 11.112 0.019 0.838 11.949
ALDH5A1
aldehyde dehydrogenase 5
family, member A1
(succinate-semialdehyde
dehydrogenase)
NM_172532 0.008−0.8088.1580.09 −0.422 8.58 0.114 0.387 8.966
CYP1A2 cytochrome P450, family 1,
subfamily A, polypeptide 2 NM_009993 0.0690.39912.7210.003−0.847 13.568 0 −1.246 12.323
CYP2A13 cytochrome P450, family 2,
subfamily A, polypeptide 13 NM_007812 0.503−0.32111.5040.02−1.399 12.903 0.052 −1.078 11.825
CYP2B6
(includes EG:1555)
cytochrome P450, family 2,
subfamily B, polypeptide 6 NM_009998 0.026−0.9482.4340.002 −1.753 4.175 0.044 −0.5462.408
CYP2B9 cytochrome P450, family 2,
subfamily b, polypeptide 9 NM_010000 0.001−5.3222.8960.684 −0.354 3.249 0.001 4.969 8.218
CYP2C38 cytochrome P450, family 2,
subfamily c, polypeptide 38 NM_010002 0.001−2.0337.6490.015 −1.247 8.896 0.079 0.7869.682
CYP2C54 cytochrome P450, family 2,
subfamily c, polypeptide 54 NM_206537 0.0190.49413.6890.088−0.32 14.01 0.002
−0.815 13.195
CYP2C55 cytochrome P450, family 2,
subfamily c, polypeptide 55 NM_028089 0.4790.2146.4310
−1.945 8.376 0 −2.1586.217
CYP2D13 cytochrome P450, family 2,
subfamily d, polypeptide 13 NR_003552 0.0050.973 6.4270.0440.582 5.845 0.141 −0.3915.454
CYP2G1P
cytochrome P450, family 2,
subfamily G, polypeptide 1
pseudogene
NM_013809 0.8740.0373.2220.002−1.19 4.411 0.001 −1.227 3.185

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 31
Continued
CYP7B1 cytochrome P450, family 7,
subfamily B, polypeptide 1 NM_007825 0.0051.46412.838 0.0131.203 11.635 0.404 −0.286 12.756
DHCR24 24-dehydrocholesterol
reductase NM_053272 0.007−1.058 11.196 0.037 −0.704 11.9 0.231 0.35412.254
HSD17B4 hydroxysteroid (17-beta)
dehydrogenase 4 NM_008292 0.007−0.6612.3080.410.149 12.159 0.003 0.809 12.968
NEDD4
neural precursor cell
expressed, developmentally
down-regulated 4
NM_010890 0.003−1.5867.5410.021 −1.061 8.602 0.127 0.433 11.085
SYVN1 synovial apoptosis
inhibitor 1, synoviolin NM_028769 0.031−1.0768.0320.790.104 7.534 0.031 1.079 9.109
Linoleic Acid Metabolism
CYP1A2 cytochrome P450, family 1,
subfamily A, polypeptide 2 NM_009993 0.0690.39912.7210.003−0.847 13.568 0 −1.246 12.323
CYP2A13 cytochrome P450, family 2,
subfamily A, polypeptide 13 NM_007812 0.503−0.321 11.5040.02−1.399 12.903 0.052 −1.07811.825
CYP2B6
(includes EG:1555)
cytochrome P450, family 2,
subfamily B, polypeptide 6 NM_009998 0.026−0.9482.4340.002 −1.753 4.175 0.044 −0.546 2.408
CYP2B9 cytochrome P450, family 2,
subfamily b, polypeptide 9 NM_010000 0.001−5.3222.8960.684 −0.354 3.249 0.001 4.9698.218
CYP2C38 cytochrome P450, family 2,
subfamily c, polypeptide 38 NM_010002 0.001−2.0337.6490.015 −1.247 8.896 0.079 0.7869.682
CYP2C54 cytochrome P450, family 2,
subfamily c, polypeptide 54 NM_206537 0.0190.49413.6890.088−0.32 14.01 0.002
−0.815 13.195
CYP2C55 cytochrome P450, family 2,
subfamily c, polypeptide 55 NM_028089 0.4790.2146.4310
−1.945 8.376 0 −2.158 6.217
CYP2D13 cytochrome P450, family 2,
subfamily d, polypeptide 13 NR_003552 0.0050.973 6.4270.0440.582 5.845 0.141 −0.391 5.454
CYP2G1P
cytochrome P450, family 2,
subfamily G, polypeptide 1
pseudogene
NM_013809 0.8740.0373.2220.002−1.19 4.411 0.001 −1.227 3.185
FADS1 fatty acid desaturase 1 NM_146094 0.005−0.92412.4360.106 −0.405 12.841 0.051 0.51913.36
FADS2 fatty acid desaturase 2 NM_019699 0.001−1.79810.5490.243 −0.399 10.947 0.002 1.482 11.893
GRN granulin NM_008175 0.014−0.86210.8890.094 −0.501 11.391 0.11 0.49310.695
PLA2G4A
phospholipase A2,
group IVA (cytosolic,
calcium-dependent)
NM_008869 0.0041.1115.765 0.013 0.879 4.886 0.396 -0.2324.654
Butanoate Metabolism
AACS acetoacetyl-CoA synthetase NM_030210 0.007−1.2157.4160.002 −1.513 8.93 0.254 −0.082 2.284
ACAT2 acetyl-Coenzyme A
acetyltransferase 2 NM_009338 0.035−0.58610.9350.005 −0.927 11.862 0.117 0.15212.068
ALDH1B1 aldehyde dehydrogenase 1
family, member B1 NM_028270 0.008−1.6066.8140.094 −0.827 7.641 0.111 0.7798.419
ALDH3A2 aldehyde dehydrogenase 3
family, member A2 NM_007437 0.048−0.65411.2960.5160.184 11.112 0.019 0.838 11.949
ALDH5A1
aldehyde dehydrogenase 5
family, member A1
(succinate-semialdehyde
dehydrogenase)
NM_172532 0.008−0.808 8.1580.09−0.422 8.58 0.114 0.387 8.966
BDH1 3-hydroxybutyrate
dehydrogenase, type 1
NM_001122683///
NM_175177 0.008 −0.9511.4880.0240.646 7.796 0.001 1.1888.984
HSD17B4 hydroxysteroid (17-beta)
dehydrogenase 4 NM_008292 0.007−0.6612.3080.410.149 12.159 0.003 0.809 12.968
Galactose Metabolism
AKR1B1
aldo-keto reductase family 1,
member B1 (aldose
reductase)
NM_009658 0.0020.852 7.9360.0260.472 7.464 0.018 −0.587 5.291
G6PC glucose-6-phosphatase,
catalytic subunit NM_008061 0.098−0.64112.0130.6410.161 11.851 0.049 0.803 12.654
GCK glucokinase (hexokinase 4) NM_010292 0.008−1.1938.6790.5110.182 8.288 0.007 1.03 9.318
HK1 hexokinase 1 NM_010438 0
−1.3483.3130.006 −0.826 4.139 0.015 −0.475 12.23

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 32
Continued
PFKL phosphofructokinase, liver NM_0088260.024−0.7348.9040.2050.363 7.152 0.006 1.0059.638
PGM1 phosphoglucomutase 1 NM_0257000.003−0.88910.729 0.142 −0.326 11.054 0.026 0.56411.618
PGM3 phosphoglucomutase 3 NM_0283520.271−0.3816.948 0.038 0.827 6.122 0.008 1.2087.329
Nicotinate Nicotinamide Metabolism
PRPF4B PRP4 pre-mRNA processing
factor 4 homolog B (yeast) NM_009873 0.039 1.332 6.1440.2540.007 2.284 0.218 −0.704 4.812
NMNAT1 nicotinamide nucleotide
adenylyltransferase 1 NM_009874 0.003 0.9446.3870.004 0.875 5.512 0.736 −0.069 5.443
PRKCE protein kinase C, epsilon NM_1334350.003−0.7844.5090.003 −0.802 5.311 0.254 0.0032.287
CDK6 cyclin-dependent kinase 6 NM_0087950.003−1.25.3020.015 −0.841 6.143 0.202 0.3596.501
PCTK3 PCTAIRE protein kinase 3 NM_0111040.001−1.3435.8720.005 −0.883 6.756 0.065 0.467.216
CDK7 cyclin-dependent kinase 7 NM_0169790.0060.7928.0310.0050.807 7.224 0.254 −0.047 2.306
PRKX protein kinase, X-linked NM_0138300.001−1.1873.9650.004−0.887 4.851 0.184 0.3 5.152
Arachidonic Acid Metabolism
ACSS2
acyl-CoA synthetase
short-chain
family member 2
NM_0198110.313 −0.52911.2180.02−1.499 12.717 0.054 −1.03 11.548
CYP1A2 cytochrome P450, family 1,
subfamily A, polypeptide 2 NM_0099930.0690.39912.721 0.003 −0.847 13.568 0 −1.246 12.323
CYP2A13 cytochrome P450, family 2,
subfamily A, polypeptide 13 NM_0078120.503 −0.32111.5040.02−1.399 12.903 0.052 −1.078 11.825
CYP2B6
(includes EG:1555)
cytochrome P450, family 2,
subfamily B, polypeptide 6 NM_0099980.026 −0.9482.4340.002−1.753 4.175 0.044 −0.546 2.408
CYP2B9 cytochrome P450, family 2,
subfamily b, polypeptide 9 NM_0100000.001 −5.3222.8960.684 −0.354 3.249 0.001 4.9698.218
CYP2C38 cytochrome P450, family 2,
subfamily c, polypeptide 38 NM_0100020.001 −2.0337.6490.015 −1.247 8.896 0.079 0.7869.682
CYP2C54 cytochrome P450, family 2,
subfamily c, polypeptide 54 NM_2065370.0190.49413.689 0.088−0.32 14.01 0.002
−0.815 13.195
CYP2C55 cytochrome P450, family 2,
subfamily c, polypeptide 55 NM_0280890.4790.2146.4310 −1.945 8.376 0 −2.158 6.217
CYP2G1P
cytochrome P450, family 2,
subfamily G, polypeptide
1 pseudogene
NM_013809 0.8740.0373.222 0.002 −1.19 4.411 0.001 −1.227 3.185
PLA2G4A
phospholipase A2,
group IVA (cytosolic,
calcium-dependent)
NM_008869 0.004 1.1115.7650.013 0.879 4.886 0.396 −0.232 4.654
Inositol Phosphate Metabolism
CDK6 cyclin-dependent kinase 6 NM_0098730.003−1.25.3020.015 −0.841 6.143 0.202 0.3596.501
CDK7 cyclin-dependent kinase 7 NM_0098740.0060.7928.0310.0050.807 7.224 0.254 −0.047 2.306
PCTK3 PCTAIRE protein kinase 3 NM_0087950.001−1.3435.8720.005 −0.883 6.756 0.065 0.467.216
PRKCE protein kinase C, epsilon NM_0111040.003−0.7844.5090.003 −0.802 5.311 0.254 0.0032.287
PRKX protein kinase, X-linked NM_0169790.001−1.1873.9650.004−0.887 4.851 0.184 0.3 5.152
PTEN
phosphatase and tensin
homolog (mutated in
multiple advanced cancers 1)
NM_0089600.005 −0.48910.369 0.026 −0.982 10.268 0.124 0.20410.859
Taurine Hypotaurine Metabolism
ACSS2
acyl-CoA synthetase
short-chain
family member 2
NM_0198110.313 −0.52911.2180.02−1.499 12.717 0.054 −1.03 11.548
CSAD cysteine sulfinic
acid decarboxylase NM_1449420.4090.31510.032 0.002 −1.786 11.818 0.001 −2.101 9.717

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 33
Supplement Table 2.
LUP/LV LUP/LC LV/LC
Name Description RefSeq ID
p-value Log2
Ratio Intensityp-valueLog2 Ratio Intensity p-value Log2 Ratio Intensity
LPS/IL-1 Mediated Inhibition of RXR Function
ALDH3A2 aldehyde dehydrogenase 3
family, member A2 NM_0074370.048 −0.65411.2960.5160.184 11.112 0.019 0.838 11.949
FABP5L2 fatty acid binding protein
5-like 2 NM_0106340.055 1.24312.1680.383−0.575 10.635 0.017 −1.969 8.666
GSTA4
glutathione S-transferase
A4 NM_0103570.4170.14910.430.003 −0.779 11.209 0.001 −0.928 10.281
ACOX1
acyl-Coenzyme A
oxidase 1, palmitoyl NM_0157290.002 −0.90113.030.298−0.207 13.236 0.008 0.69413.93
GSTM1
(includes
EG:2944)
glutathione S-transferase
M1 NM_0081830.001 −0.9978.9650 −1.162 10.127 0.332 −0.1659.962
CD14 CD14 molecule NM_0098410.0451.0276.3150.1150.755 5.56 0.534 −0.272 5.288
HS6ST1
heparan sulfate
6-O-sulfotransferase 1 NM_0158180.013−0.9977.5510.185−0.433 7.983 0.098 0.5658.548
JUN jun oncogene NM_0105910.003−1.2055.0810.390.233 4.849 0.001 1.438 6.287
FMO1
flavin containing
monooxygenase 1 NM_0102310 −1.137 10.0330.004−0.751 10.784 0.063 0.38611.171
SOD3
superoxide dismutase 3,
extracellular NM_0114350 −0.896.4290.088 −0.258 6.687 0.002 0.6317.319
FABP2
fatty acid binding protein 2,
intestinal NM_0079800.594−0.14512.1650.0350.693 11.471 0.017 0.839 12.31
SLCO1A2
solute carrier organic
anion transporter family,
member 1A2
NM_0306870.034 −1.5398.0120.025−1.668 9.68 0.828 −0.1299.551
glutathione
S-transferase A5 NM_0081810.133−1.0137.6340.001−2.393 10.925 0.004 −1.89.126GSTA5
GSTM5
glutathione
S-transferase M5 NM_0081840.376 −0.149 10.3510.002−0.818 11.169 0.005 −0.669 10.501
CYP2A13 cytochrome P450, family 2,
subfamily A, polypeptide 13 NM_0078120.503 −0.321 11.5040.02−1.399 12.903 0.052 −1.078 11.825
CYP4A14 cytochrome P450, family 4,
subfamily a, polypeptide 14 NM_0078220.04−1.50611.520.364−0.571 12.091 0.159 0.93413.026
FABP4
fatty acid binding protein 4,
adipocyte NM_0244060.254 0.0992.3830.001 1.431 6.908 0.004 1.333 9.273
GSTM4 glutathione S-transferase M4 NM_0267640.097−0.4699.2310.002−1.226 10.456 0.019 −0.757 9.699
GALNAC4S-6ST B cell RAG associated protein NM_0299350.004−0.6484.7480.001−0.814 5.562 0.29 −0.1665.396
sterol regulatory element
binding transcription factor 1 NM_0114800.003 −1.26511.290.043−0.663 11.952 0.06 0.60212.555SREBF1
GSTM3
(includes
EG:14864)
glutathione S-transferase, mu 3 NM_0103590.016−1.4169.9390.001−2.399 12.338 0.061 −0.982 11.356
NDST1
N-deacetylase/
N-sulfotransferase
(heparan glucosaminyl) 1
NM_0083060.003 −1.331 6.3960.02−0.872 7.268 0.152 0.4587.726
ATP-binding cassette,
sub-familyC
(CFTR/MRP), member3
NM_0296000.021 −1.024 9.4960.048−0.82 10.315 0.227 −0.1262.463ABCC3
cytochrome P450, family 7,
subfamily A, polypeptide 1 NM_0078240.0641.4729.6350.082−1.292 7.267 0.012 −2.2918.163CYP7A1
MGST3
microsomal glutathione
S-transferase 3 NM_0255690.131 −0.4597.7260.009−0.982 8.708 0.093 −0.5238.185
GSTM1
(includes
EG:14862)
glutathione S-transferase, mu 1 NM_0103580 −0.8613.6650 −1.256 7.021 0.016 −0.4096.612
IL1R1 interleukin 1 receptor, type I NM_0011233820.0291.579 7.2920.07 1.228 6.064 0.555 −0.3515.713
PPARA
peroxisome proliferator-
activated receptor alpha NM_0011134180.008 −1.2699.6220.7570.095 9.613 0.012 1.168 10.89
IL1B interleukin 1, beta NM_0083610.0061.6426.5060.0111.447 5.06 0.645 −0.195 4.865

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 34
Continued
SULT1C2
sulfotransferase family,
cytosolic, 1C, member 2 NM_026935 0.027−0.8736.3470.137 −0.52 6.867 0.289 0.3537.22
NR0B2
nuclear receptor subfamily 0,
group B, member 2 NM_011850 0.012−1.3959.0290.062 −0.913 9.942 0.275 0.482 10.424
FMO5
flavin containing
monooxygenase 5 NM_010232 0.001−0.88711.336 0.038−0.37 11.706 0.006 0.695 10.173
FABP7
fatty acid binding
protein 7, brain NM_021272 0.0020.876 7.3980.3870.161 7.237 0.005 −0.7156.521
ALDH1B1 aldehyde dehydrogenase
1 family, member B1 NM_028270 0.008−1.6066.8140.094−0.827 7.641 0.111 0.7798.419
ACSL3
acyl-CoA synthetase
long-chain
family member 3
NM_0010336060.011 −0.8257.6640.064 −0.519 8.184 0.233 0.3058.489
ALDH5A1
aldehyde dehydrogenase
5 family, member A1
(succinate-semialdehyde
dehydrogenase)
NM_172532 0.008−0.8088.1580.09 −0.422 8.58 0.114 0.387 8.966
PLTP phospholipid transfer protein NM_011125 0.027−1.2019.9970.011−1.493 11.49 0.51 −0.29211.198
CPT1A
carnitine palmitoyltransferase
1A (liver) NM_013495 0.008−0.83411.1370.2520.279 10.858 0.002 1.11411.972
Aryl Hydrocarbon Receptor Signaling
ALDH1B1 aldehyde dehydrogenase
1 family, member B1 NM_028270 0.008−1.6066.8140.094−0.827 7.641 0.111 0.7798.419
ALDH3A2 aldehyde dehydrogenase
3 family, member A2 NM_007437 0.048−0.65411.2960.5160.184 11.112 0.019 0.838 11.949
ALDH5A1
aldehyde dehydrogenase
5 family, member A1
(succinate-semialdehyde
dehydrogenase)
NM_172532 0.008−0.8088.1580.09 −0.422 8.58 0.114 0.387 8.966
BAX BCL2-associated X protein NM_007527 0.003−0.8446.9690.173 −0.28 7.248 0.02 0.564 7.812
CCND1 cyclin D1 NM_007631 0 −1.5995.0050 −1.239 6.244 0.041 0.3557.465
CCND2 cyclin D2 NM_009829 0.001−0.6064.1750.001−0.944 5.89 0.132 −0.1752.597
CDK6 cyclin-dependent kinase 6 NM_009873 0.003−1.25.3020.015−0.841 6.143 0.202 0.3596.501
CYP1A2
cytochrome P450, family 1,
subfamily A, polypeptide 2 NM_009993 0.0690.39912.7210.003−0.847 13.568 0 −1.246 12.323
ESR1 estrogen receptor 1 NM_007956 0.012−0.862 8.2440.02 −0.763 9.007 0.622 −0.111 4.922
FASN fatty acid synthase NM_007988 0.002−1.96111.054 0.012 −1.338 12.392 0.154 0.62313.015
GSTA4
glutathione
S-transferase A4 NM_010357 0.4170.14910.430.003−0.779 11.209 0.001 −0.92810.281
GSTA5 glutathione S-transferase A5 NM_008181 0.133−1.0137.6340.001−2.393 10.925 0.004 −1.89.126
GSTM1
(includes
EG:14862)
glutathione S-transferase, mu 1 NM_010358 0 −0.8613.6650 −1.256 7.021 0.016 −0.4096.612
GSTM1
(includes
EG:2944)
glutathione S-transferase M1 NM_008183 0.001−0.9978.9650 −1.162 10.127 0.332 −0.165 9.962
GSTM3
(includes
EG:14864)
glutathione S-transferase, mu 3 NM_010359 0.016−1.4169.9390.001−2.399 12.338 0.061 −0.98211.356
GSTM4 glutathione S-transferase M4 NM_026764 0.097−0.4699.2310.002−1.226 10.456 0.019 −0.757 9.699
GSTM5 glutathione S-transferase M5 NM_008184 0.376−0.14910.351 0.002 −0.818 11.169 0.005 −0.66910.501
IL1B interleukin 1, beta NM_008361 0.0061.6426.5060.011 1.447 5.06 0.645 −0.195 4.865
JUN jun oncogene NM_010591 0.003−1.2055.0810.390.233 4.849 0.001 1.4386.287
MGST3
microsomal glutathione
S-transferase 3 NM_025569 0.131−0.4597.7260.009−0.982 8.708 0.093 −0.523 8.185
NFIA nuclear factor I/A NM_0011229520.008−1.2347.9550.026 −0.941 8.896 0.09 0.2752.694

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 35
Continued
NFIB nuclear factor I/B NM_0011132090.001−0.88.030.005 −0.622 8.652 0.064 0.593.579
NFIC
nuclear factor I/C
(CCAAT-binding
transcription factor)
NM_008688 0.002−2.1532.8940.067 −1.007 10.325 0.009 1.4886.18
NFIX
nuclear factor I/X
(CCAAT-binding
transcription factor)
NM_0010819810.013 −0.8399.7420.049 −0.287 4.334 0.261 0.3 10.581
NQO1
NAD(P)H dehydrogenase,
quinone 1 NM_008706 0.064−0.8833.7050.035 −1.056 4.761 0.677 −0.172 4.589
NR0B2
nuclear receptor subfamily 0,
group B,
member 2
NM_011850 0.012−1.3959.0290.062 −0.913 9.942 0.275 0.482 10.424
NRIP1
nuclear receptor interacting
protein 1 NM_173440 0.003−1.2215.9190.031 −0.715 6.634 0.095 0.5067.14
SMARCA4
SWI/SNF related, matrix
associated, actin dependent
regulator of chromatin,
subfamily a, member 4
NM_011417 0.003−1.2417.7870.363 −0.302 5.462 0.004 1.198 9.028
LXR/RXR Activation
APOA4 apolipoprotein A-IV NM_007468 0.003−1.811.795 0.0141.271 10.524 0 3.071 13.595
CD14 CD14 molecule NM_009841 0.0451.0276.3150.1150.755 5.56 0.534 −0.272 5.288
CD36
CD36 molecule
(thrombospondin receptor) NM_007643 0.014−1.725.2530.432 −0.427 5.68 0.042 1.2936.973
CYP7A1
cytochrome P450, family 7,
subfamily A, polypeptide 1 NM_007824 0.0641.4729.6350.082 −1.292 7.267 0.012 −2.291 8.163
FASN fatty acid synthase NM_007988 0.002−1.96111.054 0.012 −1.338 12.392 0.154 0.62313.015
HMGCR
3-hydroxy-3-methylglutaryl-
Coenzyme A reductase NM_008255 0.428−0.2546.790.007 −1.179 7.969 0.02 −0.925 7.044
IL1B interleukin 1, beta NM_008361 0.0061.6426.506 0.0111.447 5.06 0.645 −0.195 4.865
IL1R1 interleukin 1 receptor, type I NM_0011233820.0291.5797.292 0.07 1.228 6.064 0.555 −0.3515.713
LDLR
low density lipoprotein receptor
(familial hypercholesterolemia) NM_010700 0.005−1.4579.0680.121 −0.625 9.692 0.043 0.7433.31
MSR1 macrophage scavenger receptor 1 NM_0011133260.0011.0876.7780.0140.588 6.19 0.027 −0.4995.691
PLTP phospholipid transfer protein NM_011125 0.027−1.2019.9970.011 −1.493 11.49 0.51 −0.292 11.198
SCD
stearoyl-CoA desaturase
(delta-9-desaturase) NM_009127 0.003−2.1699.6940.003 −2.087 11.781 0.596 0.10115.081
SREBF1
sterol regulatory element
binding transcription factor 1 NM_011480 0.003−1.26511.290.043 −0.663 11.952 0.06 0.60212.555
Xenobiotic Metabolism Signaling
ABCC3
ATP-binding cassette,
sub-familyC (CFTR/MRP),
member3
NM_029600 0.021−1.0249.496 0.048 −0.82 10.315 0.227 −0.126 2.463
ALDH1B1 aldehyde dehydrogenase
1 family, member B1 NM_028270 0.008−1.6066.8140.094 −0.827 7.641 0.111 0.7798.419
ALDH3A2 aldehyde dehydrogenase
3 family, member A2 NM_007437 0.048−0.65411.2960.5160.184 11.112 0.019 0.838 11.949
ALDH5A1
aldehyde dehydrogenase
5 family, member A1
(succinate-semialdehyde
dehydrogenase)
NM_172532 0.008−0.808 8.1580.09−0.422 8.58 0.114 0.387 8.966
CAMK1D
calcium/calmodulin-
dependent protein kinase ID NM_177343 0.04−0.7026.781 0.006 −1.12 7.901 0.172 −0.418 7.483
CES1
(includes
EG:12623)
carboxylesterase 1 NM_021456 0.159−0.509 9.8470.02−0.988 10.835 0.182 −0.478 10.357
CES2
(includes
EG:234671)
carboxylesterase 2 NM_145603 0.2070.33810.0190.037−0.632 10.651 0.006 −0.97 9.681
CREBBP
CREB binding protein
(Rubinstein-Taybi syndrome) NM_0010254320.005 −1.3635.9110.161 −0.511 6.422 0.018 0.0272.313

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 36
Continued
CYP1A2
cytochrome P450, family 1,
subfamily A, polypeptide 2 NM_009993 0.0690.39912.7210.003−0.847 13.568 0 −1.246 12.323
EIF2AK3
eukaryotic translation
initiation factor 2-alpha kinase 3 NM_010121 0.014−0.8055.1430.817 −0.058 5.2 0.019 0.7485.948
FMO1
flavin containing
monooxygenase 1 NM_010231 0
−1.13710.033 0.004 −0.751 10.784 0.063 0.38611.171
FMO5
flavin containing
monooxygenase 5 NM_010232 0.001−0.88711.336 0.038−0.37 11.706 0.006 0.695 10.173
GALNAC4S
-6ST B cell RAG associated protein NM_029935 0.004−0.6484.7480.001 −0.814 5.562 0.29 −0.1665.396
GSTA4 glutathione S-transferase A4 NM_010357 0.4170.14910.430.003−0.779 11.209 0.001 −0.928 10.281
GSTA5 glutathione S-transferase A5 NM_008181 0.133−1.0137.6340.001 −2.393 10.925 0.004 −1.89.126
GSTM1
(includes
EG:14862)
glutathione S-transferase, mu 1 NM_010358 0 −0.8613.6650 −1.256 7.021 0.016 −0.4096.612
GSTM1
(includes
EG:2944)
glutathione S-transferase M1 NM_008183 0.001−0.9978.9650 −1.162 10.127 0.332 −0.165 9.962
GSTM3
(includes
EG:14864)
glutathione S-transferase, mu 3 NM_010359 0.016−1.4169.9390.001 −2.399 12.338 0.061 −0.982 11.356
GSTM4 glutathione S-transferase M4 NM_026764 0.097−0.4699.2310.002−1.226 10.456 0.019 −0.757 9.699
GSTM5 glutathione S-transferase M5 NM_008184 0.376−0.14910.351 0.002 −0.818 11.169 0.005 −0.66910.501
HS6ST1
heparan sulfate
6-O-sulfotransferase 1 NM_015818 0.013−0.9977.5510.185 −0.433 7.983 0.098 0.5658.548
IL1B interleukin 1, beta NM_008361 0.0061.6426.5060.011 1.447 5.06 0.645 −0.1954.865
KEAP1
kelch-like ECH-associated
protein 1
NM_001110305
///NM_001110306
/// NM_001110307
/// NM_016679
0.005 −0.9775.1510.041 −0.593 5.744 0.054 0.269.147
MAF
v-maf musculoaponeurotic
fibrosarcoma oncogene
homolog (avian)
NM_001025577 0.007−0.8524.2640.001 −1.235 5.499 0.081 −0.334 5.989
MGST3
microsomal glutathione
S-transferase 3 NM_025569 0.131−0.4597.7260.009 −0.982 8.708 0.093 −0.523 8.185
NDST1
N-deacetylase/N-sulfotransferase
(heparan glucosaminyl) 1 NM_008306 0.003−1.3316.3960.02−0.872 7.268 0.152 0.4587.726
NQO1
NAD(P)H dehydrogenase,
quinone 1 NM_008706 0.064−0.8833.7050.035 −1.056 4.761 0.677 −0.172 4.589
NRIP1
nuclear receptor interacting
protein 1 NM_173440 0.003−1.2215.9190.031−0.715 6.634 0.095 0.5067.14
PIK3R1
phosphoinositide-3-kinase,
regulatory subunit 1 (alpha) NM_001024955 0.001−1.1246.4170.061 −0.437 3.074 0.003 0.891 7.234
PPP2R5E
protein phosphatase 2,
regulatory subunit B',
epsilon isoform
NM_012024 0 −0.9057.1870 −0.59 7.777 0.001 0.314 8.091
PRKCE protein kinase C, epsilon NM_011104 0.003−0.7844.5090.003 −0.802 5.311 0.254 0.0032.287
SOD3
superoxide dismutase 3,
extracellular NM_011435 0
−0.896.4290.088 −0.258 6.687 0.002 0.6317.319
SULT1C2
sulfotransferase family,
cytosolic, 1C, member 2 NM_026935 0.027−0.873 6.3470.137 −0.52 6.867 0.289 0.3537.22
UGT2B10 UDP glucuronosyltransferase
2 family, polypeptide B10 NM_053215 0.0241.634.538 0.104 1.041 3.497 0.322 −0.5892.908
UGT2B17 UDP glucuronosyltransferase
2 family, polypeptide B17 NM_133894 0.0073.3888.3730.107 1.639 6.734 0.075 −0.247 13.76
NRF2-mediated Oxidative Stress Response
ACTG1 actin, gamma 1 NM_009609 0.002−0.94511.9350.880.028 11.907 0.001 0.97312.88
GSTA4 glutathione S-transferase A4 NM_010357 0.4170.14910.430.003−0.779 11.209 0.001 −0.928 10.281
GSTM1
(includes
EG:2944)
glutathione S-transferase M1 NM_008183 0.001−0.9978.9650 −1.162 10.127 0.332 −0.165 9.962

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 37
Continued
DNAJC15 DnaJ (Hsp40) homolog,
subfamily C, member 15 NM_025384 0.0010.81711.0750.0130.51 10.565 0.082 −0.306 10.258
JUN jun oncogene NM_010591 0.003−1.2055.0810.390.233 4.849 0.001 1.4386.287
FMO1
flavin containing
monooxygenase 1 NM_010231 0
−1.13710.033 0.004 −0.751 10.784 0.063 0.38611.171
SOD3
superoxide dismutase 3,
extracellular NM_011435 0
−0.896.4290.088−0.258 6.687 0.002 0.6317.319
GSTA5 glutathione S-transferase A5 NM_008181 0.133−1.0137.6340.001−2.393 10.925 0.004 −1.89.126
GSTM5 glutathione S-transferase M5 NM_008184 0.376−0.14910.351 0.002 −0.818 11.169 0.005 −0.66910.501
VCP valosin-containing protein NM_009503 0.001−0.82111.941 0.361 −0.144 12.085 0.003 0.67712.762
NQO1
NAD(P)H dehydrogenase,
quinone 1 NM_008706 0.064−0.8833.7050.035−1.056 4.761 0.677 −0.172 4.589
GSTM4 glutathione S-transferase M4 NM_026764 0.097−0.4699.2310.002−1.226 10.456 0.019 −0.757 9.699
GSTM3
(includes
EG:14864)
glutathione S-transferase, mu 3 NM_010359 0.016−1.4169.9390.001−2.399 12.338 0.061 −0.98211.356
DNAJB14 DnaJ (Hsp40) homolog,
subfamily B, member 14 XM_0014731730.003 −1.2254.7 0.216−0.361 5.062 0.016 0.8645.925
MAF
v-maf musculoaponeurotic
fibrosarcoma oncogene
homolog (avian)
NM_0010255770.007 −0.8524.2640.001 −1.235 5.499 0.081 −0.334 5.989
CREBBP
CREB binding protein
(Rubinstein-Taybi syndrome) NM_0010254320.005 −1.3635.9110.161 −0.511 6.422 0.018 0.0272.313
PRKCE protein kinase C, epsilon NM_011104 0.003−0.7844.5090.003 −0.802 5.311 0.254 0.0032.287
PIK3R1
phosphoinositide-3-kinase,
regulatory subunit 1 (alpha) NM_0010249550.001 −1.1246.4170.061 −0.437 3.074 0.003 0.891 7.234
ATF4
activating transcription
factor 4 (tax-responsive
enhancer element B67)
NM_009716 0.0110.8699.160.0170.784 8.377 0.734 −0.07610.489
MGST3
microsomal glutathione
S-transferase 3 NM_025569 0.131−0.4597.7260.009 −0.982 8.708 0.093 −0.5238.185
GSTM1
(includes
EG:14862)
glutathione S-transferase, mu 1 NM_010358 0 −0.8613.6650 −1.256 7.021 0.016 −0.409 6.612
JUND jun D proto-oncogene NM_010592 0.002−0.8329.3210.115−0.309 9.63 0.02 0.52310.153
EIF2AK3
eukaryotic translation
initiation factor
2-alpha kinase 3
NM_010121 0.014−0.8055.1430.817−0.058 5.2 0.019 0.7485.948
BACH1
BTB and CNC homology 1,
basic leucine zipper t
ranscription factor 1
NM_007520 0.009−0.7614.050.004−0.915 4.965 0.038 −0.575 8.737
KEAP1
kelch-like ECH-associated
protein 1 NM_0011103050.005 −0.9775.1510.041 −0.593 5.744 0.054 0.269.147
GSK3B
glycogen synthase kinase
3 beta NM_019827 0.003−1.354.3920.027 −0.818 5.21 0.108 0.627 6.711
PXR/RXR Activation
ABCC3
ATP-binding cassette,
sub-familyC (CFTR/MRP),
member3
NM_029600 0.021−1.0249.4960.048 −0.82 10.315 0.227 −0.1262.463
ALDH3A2 aldehyde dehydrogenase 3
family, member A2 NM_007437 0.048−0.65411.2960.5160.184 11.112 0.019 0.83811.949
CPT1A
carnitine palmitoyltransferase
1A (liver) NM_013495 0.008−0.83411.1370.2520.279 10.858 0.002 1.11411.972
CYP1A2
cytochrome P450, family 1,
subfamily A, polypeptide 2 NM_009993 0.0690.39912.7210.003−0.847 13.568 0 −1.24612.323
CYP2B6
(includes
EG:1555)
cytochrome P450, family 2,
subfamily B, polypeptide 6 NM_009998 0.026−0.9482.4340.002−1.753 4.175 0.044 −0.546 2.408
CYP7A1
cytochrome P450, family 7,
subfamily A, polypeptide 1 NM_007824 0.0641.4729.6350.082−1.292 7.267 0.012 −2.291 8.163
FOXO3 forkhead box O3 NM_019740 0.01−0.8587.2860.043−0.591 7.877 0.091 −0.294.357

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 38
Continued
G6PC
glucose-6-phosphatase,
catalytic subunit NM_008061 0.098−0.64112.0130.6410.161 11.851 0.049 0.80312.654
GSTA5 glutathione S-transferase A5 NM_008181 0.133−1.0137.6340.001 −2.393 10.925 0.004 −1.8 9.126
GSTM1
(includes
EG:14862)
glutathione S-transferase, mu 1 NM_010358 0 −0.8613.6650 −1.256 7.021 0.016 −0.4096.612
GSTM1
(includes
EG:2944)
glutathione S-transferase M1 NM_008183 0.001−0.9978.9650 −1.162 10.127 0.332 −0.165 9.962
NR0B2
nuclear receptor subfamily 0,
group B, member 2 NM_011850 0.012−1.3959.0290.062 −0.913 9.942 0.275 0.482 10.424
PPARA
peroxisome proliferator-
activated receptor alpha NM_0011134180.008−1.2699.6220.7570.095 9.613 0.012 1.16810.89
PRKACA
protein kinase, cAMP-
dependent, catalytic, alpha NM_008854 0.001−0.8376.1490.164 −0.235 6.384 0.006 0.6036.986
SCD
stearoyl-CoA desaturase
(delta-9-desaturase) NM_009127 0.003−2.1699.6940.003 −2.087 11.781 0.596 0.10115.081
FXR/RXR Activation
ABCB4
ATP-binding cassette,
sub-family B (MDR/TAP),
member 4
NM_008830 0.131−0.34511.3910.0160.651 10.74 0.002 0.996 11.736
APOB
apolipoprotein B
(including Ag(x) antigen) NM_009693 0.025−1.829.830.701 −0.068 13.11 0.015 2.06411.65
CREBBP
CREB binding protein
(Rubinstein-Taybi syndrome) NM_0010254320.005−1.3635.9110.161 −0.511 6.422 0.018 0.0272.313
CYP7A1
cytochrome P450, family 7,
subfamily A, polypeptide 1 NM_007824 0.0641.4729.6350.082 −1.292 7.267 0.012 −2.291 8.163
FASN fatty acid synthase NM_007988 0.002−1.96111.054 0.012 −1.338 12.392 0.154 0.62313.015
G6PC
glucose-6-phosphatase,
catalytic subunit NM_008061 0.098−0.64112.0130.6410.161 11.851 0.049 0.80312.654
IL1B interleukin 1, beta NM_008361 0.0061.6426.5060.011 1.447 5.06 0.645 −0.195 4.865
NR0B2
nuclear receptor subfamily
0, group B, member 2 NM_011850 0.012−1.3959.0290.062 −0.913 9.942 0.275 0.482 10.424
OSTBETA organic solute transporter beta NM_178933 0 0.8033.9510 0.834 3.117 0.692 0.0313.148
PKLR pyruvate kinase, liver and RBC NM_0010997790.006−1.1799.3960.142 −0.626 8.63 0.049 0.7 10.574
PLTP phospholipid transfer protein NM_011125 0.027−1.2019.9970.011 −1.493 11.49 0.51 −0.29211.198
PPARA
peroxisome proliferator-
activated receptor alpha NM_0011134180.008−1.2699.6220.7570.095 9.613 0.012 1.16810.89
SLC22A7
solute carrier family 22
(organic anion transporter),
member 7
NM_144856 0.3040.50210.3840.0141.509 8.875 0.064 1.0079.882
SREBF1
sterol regulatory element
binding transcription factor 1 NM_011480 0.003−1.26511.290.043 −0.663 11.952 0.06 0.60212.555
VLDLR
very low density lipoprotein
receptor NM_013703 0.032−1.1593.5480.1−0.816 4.363 0.09 0.4812.856
PPARa/RXRa Activation
ACOX1
acyl-Coenzyme A oxidase 1,
palmitoyl NM_015729 0.002−0.90113.030.298 −0.207 13.236 0.008 0.69413.93
CD36
CD36 molecule
(thrombospondin receptor) NM_007643 0.014−1.725.2530.432 −0.427 5.68 0.042 1.2936.973
CREBBP
CREB binding protein
(Rubinstein-Taybi syndrome) NM_0010254320.005−1.3635.9110.161 −0.511 6.422 0.018 0.0272.313
CYP2C38 cytochrome P450, family 2,
subfamily c, polypeptide 38 NM_010002 0.001−2.0337.6490.015 −1.247 8.896 0.079 0.7869.682
CYP2C54 cytochrome P450, family 2,
subfamily c, polypeptide 54 NM_206537 0.0190.49413.6890.088−0.32 14.01 0.002
−0.815 13.195
CYP2C55 cytochrome P450, family 2,
subfamily c, polypeptide 55 NM_028089 0.4790.2146.4310
−1.945 8.376 0 −2.158 6.217
FASN fatty acid synthase NM_007988 0.002−1.96111.054 0.012 −1.338 12.392 0.154 0.62313.015

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 39
Continued
GNAQ
guanine nucleotide binding
protein (G protein),
q polypeptide
NM_008139 0.001−0.9235.9570.011−0.605 6.563 0.043 0.5146.285
GPD1
glycerol-3-phosphate
dehydrogenase 1 (soluble) NM_010271 0.003−0.86110.337 0.258 −0.227 10.565 0.012 0.63411.199
GPD2
glycerol-3-phosphate
dehydrogenase 2
(mitochondrial)
NM_010274 0.004−0.8718.9680.254−0.011 2.295 0.002 0.989 9.839
IL1B interleukin 1, beta NM_008361 0.0061.6426.5060.011 1.447 5.06 0.645 −0.1954.865
IL1R1
interleukin 1 receptor,
type I NM_001123382 0.0291.5797.292 0.07 1.228 6.064 0.555 −0.3515.713
ITGB5 integrin, beta 5 NM_010580 0.003−0.949.0490.075 −0.432 9.482 0.032 0.4749.953
JUN jun oncogene NM_010591 0.003−1.2055.0810.390.233 4.849 0.001 1.438 6.287
NR0B2
nuclear receptor subfamily 0,
group B, member 2 NM_011850 0.012−1.3959.0290.062−0.913 9.942 0.275 0.482 10.424
PPARA
peroxisome proliferator-
activated receptor alpha
NM_001113418 ///
NM_011144 0.008 −1.2699.6220.7570.095 9.613 0.012 1.168 10.89
PRKACA
protein kinase, cAMP-
dependent, catalytic, alpha NM_008854 0.001−0.8376.1490.164 −0.235 6.384 0.006 0.6036.986
SMAD3 SMAD family member 3 NM_016769 0.005−0.994.4390.105−0.438 4.877 0.052 0.5525.429
Integrin Signaling
ACTG1 actin, gamma 1 NM_009609 0.002−0.94511.9350.880.028 11.907 0.001 0.973 12.88
ARF3 ADP-ribosylation factor 3 NM_007478 0.003−0.8058.1650.181 −0.288 6.881 0.014 0.5868.97
ARHGAP26 Rho GTPase activating
protein 26 NM_175164 0.0230.7427.5740.0070.98 6.594 0.1 0.4764.812
CAPN8 calpain 8 NM_130890 0.0231.1484.2580.009 1.428 2.83 0.491 0.283.11
CAV1
caveolin 1, caveolae protein,
22 kDa NM_007616 0.0180.8727.1710.008 1.046 6.125 0.549 0.1746.3
GSK3B
glycogen synthase kinase
3 beta NM_019827 0.003−1.354.3920.027 −0.818 5.21 0.108 0.627 6.711
ITGB5 integrin, beta 5 NM_010580 0.003−0.949.0490.075 −0.432 9.482 0.032 0.4749.953
MYL9
(includes
EG:98932)
myosin, light polypeptide 9,
regulatory XM_485171 0.008−0.851 3.7260.005 −0.95 4.676 0.67 −0.14.577
PIK3R1
phosphoinositide-3-kinase,
regulatory subunit 1 (alpha) NM_001024955 0.001−1.1246.4170.061 −0.437 3.074 0.003 0.891 7.234
PTEN
phosphatase and tensin
homolog (mutated in
multiple advanced cancers 1)
NM_008960 0.005−0.48910.369 0.026 −0.982 10.268 0.124 0.20410.859
PXN paxillin NM_011223 0.002−1.1469.1790.031 −0.633 9.812 0.064 0.513 10.325
RAP1B
RAP1B, member of RAS
oncogene family NM_024457 0.0011.046 9.9140.020.595 9.319 0.055 −0.4518.868
RAPGEF1 Rap guanine nucleotide
exchange factor (GEF) 1 NM_001039086 0.031−0.8554.5580.586 −0.178 4.736 0.069 0.6775.413
RHOJ
ras homolog gene family,
member J NM_023275 0.001−1.5534.1050.011 −0.882 4.987 0.033 0.6715.658
RHOU
ras homolog gene family,
member U NM_133955 0
−1.2218.9330.021 −0.436 9.368 0.001 0.785 10.154
RND2 Rho family GTPase 2 NM_009708 0.009−0.5837.4850.001−0.859 8.343 0.128 −0.2768.067
VCL vinculin NM_009502 0.007−0.8527.9540.158 −0.352 8.305 0.061 0.5018.806
WAS
Wiskott-Aldrich syndrome
(eczema-thrombocytopenia) NM_009515 0.0220.8074.520.0640.597 3.923 0.46 −0.213.713
WASL
(includes
EG:8976)
Wiskott-Aldrich syndrome-like NM_028459 0.001−0.8086.7960.016 −0.251 9.173 0.007 0.5497.604
ZYX zyxin NM_011777 0.003−1.2796.5490.007−1.097 7.646 0.538 0.1827.828
RXR Activation

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 40
Continued
CCNH cyclin H NM_023243 0.0030.911 7.3310.0520.479 6.852 0.043 −0.306 8.953
CDK7 cyclin-dependent kinase 7 NM_009874 0.0060.7928.0310.0050.807 7.224 0.254 −0.047 2.306
CREBBP
CREB binding protein
(Rubinstein-Taybi syndrome) NM_0010254320.005 −1.3635.9110.161 −0.511 6.422 0.018 0.0272.313
CSNK2A1 casein kinase 2, alpha 1
polypeptide NM_007788 0.001−1.0877.1110.015 −0.604 7.715 0.036 0.4838.198
CYP26A1 cytochrome P450, family 26,
subfamily A, polypeptide 1 NM_007811 0.022−1.9915.1920.001 −3.72 8.911 0.037 −1.729 7.183
DUSP1 dual specificity phosphatase 1 NM_013642 0.005−1.4267.3980.5860.197 7.201 0.003 1.623 8.824
JUN jun oncogene NM_010591 0.003−1.2055.0810.390.233 4.849 0.001 1.4386.287
NR2F2
nuclear receptor subfamily 2,
group F, member 2 NM_009697 0.004−0.8857.7920.01 −0.725 8.518 0.067 0.1012.422
NRIP1
nuclear receptor
interacting protein 1 NM_173440 0.003−1.2215.9190.031 −0.715 6.634 0.095 0.5067.14
PIK3R1
phosphoinositide-3-kinase,
regulatory subunit 1 (alpha) NM_0010249550.001 −1.1246.4170.061 −0.437 3.074 0.003 0.8917.234
PRKACA
protein kinase, cAMP-
dependent, catalytic, alpha NM_008854 0.001−0.8376.1490.164 −0.235 6.384 0.006 0.6036.986
PRKCE protein kinase C, epsilon NM_011104 0.003−0.7844.5090.003 −0.802 5.311 0.254 0.0032.287
PTEN
phosphatase and tensin
homolog (mutated in multiple
advanced cancers 1)
NM_008960 0.005−0.48910.369 0.026 −0.982 10.268 0.124 0.20410.859
RDH11
retinol dehydrogenase 11
(all-trans/9-cis/11-cis) NM_021557 0.697−0.143 8.3210.02 −1.089 9.41 0.034 −0.945 8.464
RDH16
(includes
EG:19683)
retinol dehydrogenase 16 NM_009040 0.031−0.9788.0010.066 −0.783 8.784 0.6 0.1958.979
SMAD3 SMAD family member 3 NM_016769 0.005−0.994.4390.105 −0.438 4.877 0.052 0.5525.429
SMAD6 SMAD family member 6 NM_008542 0.015−0.9064.7420.069 −0.595 5.337 0.294 0.3115.647
SMARCA2
SWI/SNF related, matrix
associated, actin dependent
regulator of chromatin,
subfamily a, member 2
NM_011416 0.023−0.8894.8370.4360.004 2.325 0.063 0.6745.726
SMARCA4
SWI/SNF related, matrix
associated, actin dependent
regulator of chromatin,
subfamily a, member 4
NM_011417 0.003−1.2417.7870.363 −0.302 5.462 0.004 1.1989.028
STAT5A
signal transducer and activator
of transcription 5A NM_011488 0.009−0.682.8560.1160.493 5.449 0.003 0.83 3.536
P53 Signaling
BAX BCL2-associated X protein NM_007527 0.003−0.8446.9690.173 −0.28 7.248 0.02 0.564 7.812
CCND1 cyclin D1 NM_007631 0 −1.5995.0050 −1.239 6.244 0.041 0.3557.465
CCND2 cyclin D2 NM_009829 0.001−0.6064.1750.001−0.944 5.89 0.132 −0.175 2.597
FASN fatty acid synthase NM_007988 0.002−1.96111.054 0.012 −1.338 12.392 0.154 0.62313.015
GSK3B glycogen synthase kinase 3 beta NM_019827 0.003−1.354.3920.027 −0.818 5.21 0.108 0.627 6.711
HIPK2
homeodomain interacting
protein kinase 2 NM_010433 0.013−1.5796.1490.105 −0.872 7.021 0.04 0.5715.961
JUN jun oncogene NM_010591 0.003−1.2055.0810.390.233 4.849 0.001 1.4386.287
PIK3R1
phosphoinositide-3-kinase,
regulatory subunit 1 (alpha) NM_0010249550.001 −1.1246.4170.061 −0.437 3.074 0.003 0.8917.234
PLAGL1
pleiomorphic adenoma
gene-like 1 NM_009538 0.002−1.833.9040.093 −0.729 4.633 0.023 1.1015.734
PTEN
phosphatase and tensin
homolog (mutated in multiple
advanced cancers 1)
NM_008960 0.005−0.48910.369 0.026 −0.982 10.268 0.124 0.20410.859
TP53BP2
tumor protein p53 binding
protein, 2 NM_173378 0.001−0.8354.350.1690.145 6.649 0.003 0.695 5.185

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 41
Continued
Nucleotide Excision Repair Pathway
CCNH cyclin H NM_023243 0.0030.911 7.3310.0520.479 6.852 0.043 −0.3068.953
CDK7 cyclin-dependent kinase 7 NM_009874 0.0060.7928.0310.0050.807 7.224 0.254 −0.047 2.306
ERCC8
excision repair cross-
complementing
rodent repair deficiency,
complementation group 8
NM_028042 0.0270.8555.1840.0550.703 4.481 0.133 −0.1523.782
POLR2A
polymerase (RNA) II
(DNA directed)
polypeptide A, 220 kDa
NM_009089 0.025−1.0225.640.618 −0.183 5.822 0.051 0.839 6.661
POLR2C
polymerase (RNA) II
(DNA directed)
polypeptide C, 33 kDa
NM_009090 0.0050.8569.0710.0580.467 8.604 0.1 −0.389 8.215
RPA3 replication protein A3, 14 kDa NM_026632 0.0121.0068.220.2280.387 7.833 0.074 −0.619 7.215
ERK/MAPK Signaling
PPP1R14A
protein phosphatase 1,
regulatory (inhibitor)
subunit 14A
NM_026731 0.0140.8685.6720.0520.618 5.054 0.371 −0.25 4.805
YWHAG
tyrosine 3-monooxygenase/
tryptophan 5-monooxygenase
activation protein,
gamma polypeptide
NM_018871 0.001−0.9178.8570.032 −0.405 9.262 0.012 0.5129.774
MKNK2
MAP kinase interacting
serine/threonine kinase 2 NM_021462 0.005−1.5829.2580.012 −1.316 10.574 0.323 0.3355.522
RAP1B
RAP1B, member of RAS
oncogene family NM_024457 0.0011.0469.9140.020.595 9.319 0.055 −0.451 8.868
DUSP1 dual specificity phosphatase 1 NM_013642 0.005−1.4267.3980.5860.197 7.201 0.003 1.623 8.824
PPP2R5E
protein phosphatase 2,
regulatory subunit B’,
epsilon isoform
NM_012024 0 −0.9057.1870 −0.59 7.777 0.001 0.314 8.091
RAPGEF1 Rap guanine nucleotide
exchange factor (GEF) 1 NM_0010390860.031 −0.8554.5580.586 −0.178 4.736 0.069 0.6775.413
PRKCE protein kinase C, epsilon NM_011104 0.003−0.7844.5090.003−0.802 5.311 0.254 0.0032.287
PRKACA
protein kinase, cAMP-
dependent, catalytic, alpha NM_008854 0.001−0.8376.1490.164−0.235 6.384 0.006 0.6036.986
PIK3R1
Phosphoinositide-3-kinase,
regulatory subunit 1 (alpha) NM_0010249550.001 −1.1246.4170.061 −0.437 3.074 0.003 0.891 7.234
ESR1 estrogen receptor 1 NM_007956 0.012−0.8628.2440.02 −0.763 9.007 0.622 −0.1114.922
PXN paxillin NM_011223 0.002−1.1469.1790.031 −0.633 9.812 0.064 0.513 10.325
MAP2K1IP1
mitogen-activated protein
kinase kinase 1 interacting
protein 1
NM_019920 0.010.8059.7960.0530.53 9.265 0.263 −0.275 8.991
ATF4
activating transcription
factor 4 (tax-responsive
enhancer element B67)
NM_009716 0.0110.8699.160.0170.784 8.377 0.734 −0.076 10.489
MYCN
v-myc myelocytomatosis
viral related oncogene,
neuroblastoma derived (avian)
NM_008709 0.127−0.7684.1130.234 −0.054 2.357 0.035 1.167 4.881
PLA2G4A phospholipase A2, group IVA
(cytosolic, calcium-dependent) NM_008869 0.0041.1115.765 0.013 0.879 4.886 0.396 −0.232 4.654
ELK3
ELK3, ETS-domain protein
(SRF accessory protein 2) NM_013508 0.01−0.6035.5670.002 −0.849 6.415 0.033 0.4554.877
RPS6KA1 ribosomal protein S6 kinase,
90 kDa, polypeptide 1 NM_009097 0.007−1.0495.9430.209 −0.369 6.312 0.04 0.6816.993
PPP1R3C
protein phosphatase 1,
regulatory (inhibitor)
subunit 3C
NM_016854 0.292−0.27611.7890.0630.63 7.723 0.014 0.805 12.065
Hepatic Cholestasis

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 42
Continued
ABCB4
ATP-binding cassette, sub-
family B (MDR/TAP),
member 4
NM_008830 0.131−0.34511.3910.0160.651 10.74 0.002 0.996 11.736
ABCC3
ATP-binding cassette,
sub-familyC (CFTR/MRP),
member3
NM_029600 0.021−1.0249.496 0.048 −0.82 10.315 0.227 −0.1262.463
CD14 CD14 molecule NM_009841 0.0451.0276.3150.1150.755 5.56 0.534 −0.2725.288
CYP7A1
cytochrome P450,
family 7, subfamily
A, polypeptide 1
NM_007824 0.0641.4729.6350.082 −1.292 7.267 0.012 −2.291 8.163
CYP7B1
cytochrome P450,
family 7, subfamily
B, polypeptide 1
NM_007825 0.0051.46412.838 0.0131.203 11.635 0.404 −0.28612.756
ESR1 estrogen receptor 1 NM_007956 0.012−0.862 8.2440.02−0.763 9.007 0.622 −0.111 4.922
IL1B interleukin 1, beta NM_008361 0.0061.6426.506 0.011 1.447 5.06 0.645 −0.195 4.865
IL1R1
interleukin 1 receptor,
type I NM_0011233820.029 1.5797.292 0.07 1.228 6.064 0.555 −0.351 5.713
JUN jun oncogene NM_010591 0.003−1.2055.0810.390.233 4.849 0.001 1.4386.287
NR0B2
nuclear receptor subfamily 0,
group B, member 2 NM_011850 0.012−1.3959.0290.062 −0.913 9.942 0.275 0.48210.424
PPARA
peroxisome proliferator-
activated receptor alpha NM_0011134180.008 −1.2699.6220.7570.095 9.613 0.012 1.168 10.89
PRKACA
protein kinase, cAMP-
dependent, catalytic, alpha NM_008854 0.001−0.8376.1490.164 −0.235 6.384 0.006 0.6036.986
PRKCE protein kinase C, epsilon NM_011104 0.003−0.7844.5090.003 −0.802 5.311 0.254 0.0032.287
SLC22A7
solute carrier family 22
(organic anion transporter),
member 7
NM_144856 0.3040.50210.3840.0141.509 8.875 0.064 1.007 9.882
SLCO1A2
solute carrier organic
anion transporter family,
member 1A2
NM_030687 0.034−1.5398.0120.025 −1.668 9.68 0.828 −0.129 9.551
SREBF1
sterol regulatory element
binding transcription factor 1 NM_011480 0.003−1.26511.290.043 −0.663 11.952 0.06 0.60212.555
Glucocorticoid Receptor Signaling
AR
androgen receptor
(dihydrotestosterone receptor;
testicular feminization; spinal
and bulbar muscular atrophy;
Kennedy disease)
NM_013476 0.007−0.933.522 0.002 −1.25 4.772 0.061 −0.626 5.533
CCL5 chemokine (C-C motif) ligand 5 NM_013653 0.6030.1254.0880.008−0.878 4.965 0.004 −1.003 3.963
CCNH cyclin H NM_023243 0.0030.911 7.3310.0520.479 6.852 0.043 −0.306 8.953
CDK7 cyclin-dependent kinase 7 NM_009874 0.0060.7928.0310.0050.807 7.224 0.254 −0.047 2.306
CREBBP
CREB binding protein
(Rubinstein-Taybi syndrome) NM_0010254320.005 −1.3635.9110.161 −0.511 6.422 0.018 0.0272.313
DUSP1 dual specificity phosphatase 1 NM_013642 0.005−1.4267.3980.5860.197 7.201 0.003 1.623 8.824
ESR1 estrogen receptor 1 NM_007956 0.012−0.862 8.2440.02−0.763 9.007 0.622 −0.111 4.922
FCGR1A
Fc fragment of IgG, high
affinity Ia, receptor (CD64) NM_010186 0.0031 6.6980.10.421 6.276 0.037 −0.5795.698
GTF2A2
general transcription factor
IIA, 2, 12 kDa NM_0010395190.0031.047 9.8990.0480.562 9.337 0.077 −0.485 8.852
HSPA4 heat shock 70 kDa protein 4 NM_008300 0.011−0.4249.2 0.15−0.194 9.394 0.016 1.2517.18
IL1B interleukin 1, beta NM_008361 0.0061.6426.506 0.011 1.447 5.06 0.645 −0.195 4.865
JUN jun oncogene NM_010591 0.003−1.2055.0810.390.233 4.849 0.001 1.4386.287
NRIP1
nuclear receptor interacting
protein 1 NM_173440 0.003−1.2215.9190.031 −0.715 6.634 0.095 0.5067.14
PBX1 pre-B-cell leukemia homeobox 1 NM_008783 0.004−1.1185.6350.042 −0.63 6.265 0.093 0.488 6.753

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 43
Continued
PIK3R1
phosphoinositide-3-kinase,
regulatory subunit 1 (alpha) NM_001024955 0.001−1.1246.417 0.061−0.437 3.074 0.003 0.891 7.234
POLR2A
polymerase (RNA) II
(DNA directed)
polypeptide A, 220 kDa
NM_009089 0.025−1.0225.640.618 −0.183 5.822 0.051 0.839 6.661
POLR2C
polymerase (RNA) II
(DNA directed)
polypeptide C, 33 kDa
NM_009090 0.0050.8569.0710.0580.467 8.604 0.1 −0.389 8.215
PRKACA
protein kinase, cAMP-
dependent, catalytic, alpha NM_008854 0.001−0.8376.149 0.164−0.235 6.384 0.006 0.6036.986
SMAD3 SMAD family member 3 NM_016769 0.005−0.994.439 0.105−0.438 4.877 0.052 0.5525.429
SMARCA2
SWI/SNF related, matrix
associated, actin dependent
regulator of chromatin,
subfamily a, member 2
NM_011416 0.023−0.8894.8370.436 0.004 2.325 0.063 0.674 5.726
SMARCA4
SWI/SNF related, matrix
associated, actin dependent
regulator of chromatin,
subfamily a, member 4
NM_011417 0.003−1.2417.787 0.363−0.302 5.462 0.004 1.198 9.028
STAT5A
signal transducer and activator
of transcription 5A NM_011488 0.009−0.682.8560.116 0.493 5.449 0.003 0.833.536
TBP TATA box binding protein NM_013684 0.0040.8636.324 0.0020.98 5.344 0.576 0.1175.461
NFkB Signaling
CARD10
caspase recruitment domain
family, member 10 NM_130859 0
−1.275.419 0.001−0.993 6.413 0.142 0.2766.689
CREBBP
CREB binding protein
(Rubinstein-Taybi syndrome) NM_001025432 0.005−1.3635.911 0.161−0.511 6.422 0.018 0.0272.313
CSNK2A1 casein kinase 2, alpha 1
polypeptide NM_007788 0.001−1.0877.111 0.015−0.604 7.715 0.036 0.4838.198
EGFR
epidermal growth factor
receptor (erythroblastic
leukemia viral (v-erb-b)
oncogene homolog, avian)
NM_007912 0.0091.05310.54 0.0351.053 9.481 0.039 −0.733 9.487
GSK3B
glycogen synthase kinase
3 beta NM_019827 0.003−1.354.392 0.027−0.818 5.21 0.108 0.627 6.711
IL1B interleukin 1, beta NM_008361 0.0061.6426.506 0.0111.447 5.06 0.645 −0.1954.865
IL1R1 interleukin 1 receptor, type I NM_001123382 0.0291.5797.2920.071.228 6.064 0.555 −0.351 5.713
KLK1B4 kallikrein 1-related pepidase b4 NM_010915 0.202−0.4114.4570.03−0.808 5.265 0.216 −0.397 4.869
PDGFRB
platelet-derived growth factor
receptor, beta polypeptide NM_008809 0
−1.1445.035 0.007−0.598 5.633 0.01 0.5466.179
PIK3R1
phosphoinositide-3-kinase,
regulatory subunit 1 (alpha) NM_001024955 0.001−1.1246.417 0.061−0.437 3.074 0.003 0.891 7.234
PRKACA
protein kinase, cAMP-
dependent, catalytic, alpha NM_008854 0.001−0.8376.149 0.164−0.235 6.384 0.006 0.6036.986
TGFA
transforming growth
factor, alpha NM_031199 0.011−0.8916.539 0.051−0.604 7.143 0.254 −0.099 2.284
TRAF3
TNF receptor-associated
factor 3 NM_001048206 0.018−1.5534.619 0.272−0.176 2.538 0.014 1.636 6.172
IL−10 Signaling
BLVRA biliverdin reductase A NM_026678 0.0000.8409.0770.001 0.535 8.542 0.015 −0.305 8.237
CD14 CD14 molecule NM_009841 0.0451.027 6.3150.115 0.755 5.560 0.534 −0.272 5.288
FCGR2A
Fc fragment of IgG, low
affinity IIa, receptor (CD32) NM_010188 0.0011.3337.1160.038 0.542 6.574 0.008 −0.791 5.783
IL1B interleukin 1, beta NM_008361 0.0061.6426.506 0.0111.447 5.060 0.645 −0.195 4.865
IL1R1 interleukin 1 receptor, type I NM_001123382
/// NM_008362 0.029 1.5797.292 0.0701.228 6.064 0.555 −0.351 5.713
JUN jun oncogene NM_010591 0.003−1.2055.0810.390 0.233 4.849 0.001 1.438 6.287
SOCS3
suppressor of cytokine
signaling 3 NM_007707 0.0060.9005.801 0.0001.482 4.318 0.039 0.5824.901

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 44
Continued
PTEN Signaling
BCL2L11
BCL2-like 11
(apoptosis facilitator) NM_009754 0.006−1.1033.9510.193−0.311 2.762 0.035 0.7155.053
CCND1 cyclin D1 NM_007631 0 −1.5995.0050 −1.239 6.244 0.041 0.3557.465
CSNK2A1 casein kinase 2, alpha 1
polypeptide NM_007788 0.001−1.0877.1110.015−0.604 7.715 0.036 0.4838.198
EGFR
epidermal growth factor
receptor (erythroblastic
leukemia viral (v-erb-b)
oncogene homolog, avian)
NM_007912 0.0091.05310.54 0.0351.053 9.481 0.039 −0.7339.487
FOXO3 forkhead box O3 NM_019740 0.01−0.8587.2860.043 −0.591 7.877 0.091 −0.29 4.357
GSK3B
glycogen synthase kinase
3 beta NM_019827 0.003−1.354.3920.027−0.818 5.21 0.108 0.627 6.711
INPPL1
inositol polyphosphate
phosphatase-like 1 NM_0011227390.006 −0.9815.2240.058 −0.561 5.785 0.132 0.426.205
PDGFRB
platelet-derived growth
factor receptor,
beta polypeptide
NM_008809 0 −1.1445.0350.007 −0.598 5.633 0.01 0.5466.179
PIK3R1
phosphoinositide-3-kinase,
regulatory subunit 1 (alpha) NM_0010249550.001 −1.1246.4170.061 −0.437 3.074 0.003 0.8917.234
PTEN
phosphatase and tensin
homolog (mutated in
multiple advanced cancers 1)
NM_008960 0.005−0.48910.3690.026 −0.982 10.268 0.124 0.20410.859
Estrogen Receptor Signaling
CCNH cyclin H NM_023243 0.0030.911 7.3310.0520.479 6.852 0.043 −0.3068.953
CDK7 cyclin-dependent kinase 7 NM_009874 0.0060.7928.0310.0050.807 7.224 0.254 −0.0472.306
CREBBP
CREB binding protein
(Rubinstein-Taybi syndrome) NM_0010254320.005 −1.3635.9110.161−0.511 6.422 0.018 0.0272.313
ESR1 estrogen receptor 1 NM_007956 0.012−0.8628.2440.02 −0.763 9.007 0.622 −0.1114.922
G6PC
glucose-6-phosphatase,
catalytic subunit NM_008061 0.098−0.64112.0130.6410.161 11.851 0.049 0.80312.654
HNRPD
heterogeneous nuclear
ribonucleoprotein D
(AU-rich element RNA
binding protein 1, 37 kDa)
NM_0010772650.004 −0.9187.3720.064 −0.283 4.374 0.064 0.4728.289
NR0B2
nuclear receptor subfamily 0,
group B, member 2 NM_011850 0.012−1.3959.0290.062−0.913 9.942 0.275 0.482 10.424
NRIP1
nuclear receptor interacting
protein 1 NM_173440 0.003−1.2215.9190.031−0.715 6.634 0.095 0.5067.14
POLR2A
polymerase (RNA) II
(DNA directed)
polypeptide A, 220 kDa
NM_009089 0.025−1.0225.640.618 −0.183 5.822 0.051 0.8396.661
POLR2C
polymerase (RNA) II
(DNA directed)
polypeptide C, 33 kDa
NM_009090 0.0050.8569.0710.0580.467 8.604 0.1 −0.389 8.215
SMARCA4
SWI/SNF related, matrix
associated, actin dependent
regulator of chromatin,
subfamily a, member 4
NM_011417 0.003−1.2417.7870.363−0.302 5.462 0.004 1.1989.028
TBP TATA box binding protein NM_013684 0.0040.8636.324 0.0020.98 5.344 0.576 0.1175.461
14-3-3 mediated Signaling
AKT1S1
AKT1 substrate 1
(proline-rich) NM_026270 0.013−1.1457.5360.155 −0.541 8.077 0.094 0.4645.732
BAX BCL2-associated X protein NM_007527 0.003−0.8446.9690.173 −0.28 7.248 0.02 0.564 7.812
EGFR
epidermal growth factor
receptor (erythroblastic
leukemia viral (v-erb-b)
oncogene homolog, avian)
NM_007912 0.0091.05310.54 0.0351.053 9.481 0.039 −0.7339.487
GSK3B
glycogen synthase kinase
3 beta NM_019827 0.003−1.354.3920.027−0.818 5.21 0.108 0.627 6.711

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 45
Continued
JUN jun oncogene NM_010591 0.003−1.2055.0810.390.233 4.849 0.001 1.438 6.287
PDGFRB
platelet-derived growth
factor receptor,
beta polypeptide
NM_008809 0 −1.1445.0350.007 −0.598 5.633 0.01 0.5466.179
PIK3R1
phosphoinositide-3-kinase,
regulatory subunit 1 (alpha) NM_0010249550.001 −1.1246.4170.061 −0.437 3.074 0.003 0.8917.234
PRKCE protein kinase C, epsilon NM_011104 0.003−0.7844.5090.003 −0.802 5.311 0.254 0.0032.287
RPS6KA1 ribosomal protein S6 kinase,
90 kDa, polypeptide 1 NM_009097 0.007−1.0495.9430.209 −0.369 6.312 0.04 0.6816.993
SNCA
synuclein, alpha (non A4
component of amyloid
precursor)
NM_0010424510.022 −1.0438.3160.003 −1.596 9.912 0.126 −0.59 9.648
TUBB2A tubulin, beta 2A NM_009450 0 −1.3510.8680.4540.196 4.976 0 1.3212.219
YWHAG
tyrosine 3-monooxygenase/
tryptophan 5-monooxygenase
activation protein,
gamma polypeptide
NM_018871 0.001−0.9178.8570.032 −0.405 9.262 0.012 0.5129.774
PPAR Signaling
CREBBP
CREB binding protein
(Rubinstein-Taybi syndrome) NM_0010254320.005 −1.3635.9110.161 −0.511 6.422 0.018 0.0272.313
IL1B interleukin 1, beta NM_008361 0.0061.6426.5060.011 1.447 5.06 0.645 −0.195 4.865
IL1R1 interleukin 1 receptor, type I NM_0011233820.0291.5797.292 0.07 1.228 6.064 0.555 −0.351 5.713
JUN jun oncogene NM_010591 0.003−1.2055.0810.390.233 4.849 0.001 1.438 6.287
NR0B2
nuclear receptor subfamily 0,
group B, member 2 NM_011850 0.012−1.3959.0290.062 −0.913 9.942 0.275 0.482 10.424
NRIP1
nuclear receptor interacting
protein 1 NM_173440 0.003−1.2215.9190.031 −0.715 6.634 0.095 0.5067.14
PDGFRB
platelet-derived growth factor
receptor, beta polypeptide NM_008809 0
−1.1445.0350.007 −0.598 5.633 0.01 0.5466.179
PPARA
peroxisome proliferator-
activated receptor alpha NM_0011134180.008 −1.2699.6220.7570.095 9.613 0.012 1.168 10.89
STAT5A
signal transducer and activator
of transcription 5A NM_011488 0.009−0.682.8560.1160.493 5.449 0.003 0.83 3.536
TR/RXR Activation
CYP7A1
cytochrome P450, family 7,
subfamily A, polypeptide 1 NM_007824 0.0641.4729.6350.082 −1.292 7.267 0.012 −2.291 8.163
DIO1 deiodinase, iodothyronine, type I NM_007860 0.110.41812.4320 1.671 10.761 0.001 1.253 12.014
FASN fatty acid synthase NM_007988 0.002−1.96111.054 0.012 −1.338 12.392 0.154 0.62313.015
G6PC
Glucose-6-phosphatase,
catalytic subunit NM_008061 0.098−0.64112.0130.6410.161 11.851 0.049 0.803 12.654
LDLR
low density lipoprotein receptor
(familial hypercholesterolemia) NM_010700 0.005−1.4579.0680.121 −0.625 9.692 0.043 0.7433.31
ME1
malic enzyme 1,
NADP(+)-dependent,
cytosolic
NM_008615 0.012−1.13711.440.017 −1.058 12.499 0.7 −0.172 11.28
PIK3R1
Phosphoinositide-3-kinase,
regulatory subunit 1 (alpha) NM_0010249550.001 −1.1246.4170.061 −0.437 3.074 0.003 0.8917.234
RCAN2 regulator of calcineurin 2 NM_030598 0 −2.6675.180.018 −0.922 6.101 0.001 1.7467.847
SLC2A1
solute carrier family 2
(facilitated glucose
transporter), member 1
NM_011400 0.034−0.838 4.4090.04−0.799 5.208 0.693 0.094.814
SREBF1
sterol regulatory element
binding transcription factor 1 NM_011480 0.003−1.26511.290.043 −0.663 11.952 0.06 0.60212.555
THRSP
thyroid hormone responsive
(SPOT14 homolog, rat) NM_009381 0.099−0.6713.337 0.042 −0.883 14.219 0.477 −0.35 11.878
UCP2
uncoupling protein 2
(mitochondrial, proton carrier) NM_011671 0.032−0.6086.7140.007 −0.881 7.595 0.26 −0.273 7.322
Cell Cycle: G1/S Checkpoint Regulation

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 46
Continued
CCND1 cyclin D1 NM_007631 0 −1.5995.0050 −1.239 6.244 0.041 0.3557.465
CCND2 cyclin D2 NM_009829 0.001−0.6064.175 0.001−0.944 5.89 0.132 −0.175 2.597
CDK6 Cyclin-dependent kinase 6 NM_009873 0.003−1.25.302 0.015−0.841 6.143 0.202 0.3596.501
GSK3B
glycogen synthase kinase
3 beta NM_019827 0.003−1.354.392 0.027−0.818 5.21 0.108 0.6276.711
SMAD3 SMAD family member 3 NM_016769 0.005−0.994.439 0.105−0.438 4.877 0.052 0.5525.429
IL-2 Signaling
CSNK2A1 casein kinase 2, alpha 1
polypeptide NM_007788 0.001−1.0877.111 0.015−0.604 7.715 0.036 0.4838.198
JUN jun oncogene NM_010591 0.003−1.2055.0810.390.233 4.849 0.001 1.438 6.287
PIK3R1
Phosphoinositide-3-kinase,
regulatory subunit 1 (alpha) NM_0010249550.001 −1.1246.417 0.061−0.437 3.074 0.003 0.8917.234
STAT5A
signal transducer and activator
of transcription 5A NM_011488 0.009−0.682.8560.1160.493 5.449 0.003 0.83 3.536
JAK/Stat Signaling
PIK3R1
Phosphoinositide-3-kinase,
regulatory subunit 1 (alpha) NM_0010249550.001 −1.1246.417 0.061−0.437 3.074 0.003 0.8917.234
SOCS2
suppressor of cytokine
signaling 2 NM_007706 0.0032.468.840.2540.074 2.291 0.005 −1.893 6.011
SOCS3
suppressor of cytokine
signaling 3 NM_007707 0.0060.9 5.801 0 1.482 4.318 0.039 0.5824.901
STAT5A
signal transducer and activator
of transcription 5A NM_011488 0.009−0.682.8560.1160.493 5.449 0.003 0.83 3.536
IL-4 Signaling
HLA-DMA major histocompatibility
complex, class II, DM alpha NM_010386 0.0680.5325.7990.308−0.268 6.068 0.015 −0.8 5.268
HLA-DQB2 major histocompatibility
complex, class II, DQ beta 2 NM_207105 0.793−0.1276.4240.025−1.355 7.779 0.036 −1.2286.551
HLA-DRB1 major histocompatibility
complex, class II, DR beta 1 NM_010382 0.903−0.0688.855 0.045−1.327 10.182 0.054 −1.26 8.923
IL13RA1 interleukin 13 receptor, alpha 1 NM_133990 0.0071.0887.8980.0490.681 7.217 0.116 −0.452 7.264
INPPL1
inositol polyphosphate
phosphatase-like 1 NM_0011227390.006 −0.9815.224 0.058−0.561 5.785 0.132 0.426.205
PIK3R1
Phosphoinositide-3-kinase,
regulatory subunit 1 (alpha) NM_0010249550.001 −1.1246.417 0.061−0.437 3.074 0.003 0.8917.234
Antigen Presentation Pathway
CD74
CD74 molecule, major
histocompatibility complex,
class II invariant chain
NM_0010426050.219 −0.5119.262 0.017−1.202 10.464 0.112 −0.691 9.773
HLA-DMA major histocompatibility
complex, class II, DM alpha NM_010386 0.0680.5325.7990.308−0.268 6.068 0.015 −0.8 5.268
HLA-DQB2 major histocompatibility
complex, class II, DQ beta 2 NM_207105 0.793−0.1276.4240.025−1.355 7.779 0.036 −1.2286.551
HLA-DRB1 major histocompatibility
complex, class II, DR beta 1 NM_010382 0.903−0.0688.855 0.045−1.327 10.182 0.054 −1.26 8.923
the total number of genes known to be associated with
that pathway, 3) the total number of eligible genes in-
cluded in the analysis, and 4) the total number of genes
in the input data. Tables of −log(p-value), to rank the sig-
nificance, were exported from IPA into JavaTreeView
[10] to generate heatmaps (Supplement Figure 4). IPA
presents pathway analysis data in part as interactive
graphs. Pathway graphs deemed to be highly significant
to UP780 mechanism of action are illustrated in the
Supplement Figures 5 and 6. In addition, genes inclu-
ded in the significant pathways from all three contrasts
were exported to Excel as Supplement Tables 1-4.
From the Ingenuity pathway analysis result of signifi-
cant Canonical Pathways, the p-values derived from the
evaluation of the pathways in association with the gene
expression variations were −log10 transformed and plot-
ted as heatmaps [10], for liver metabolic pathways (Sup-
plement Figure 4(a)) and signaling pathways (Supple-
ment Figure 4(b)) and for WAT metabolic pathways
(Supplement Figure 4(c)) and signaling pathways (Sup-
plement Figure 4(d)). The complete gene lists for indi-
vidual pathways in Supplement Figure 4 are supplied as

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 47
(a) (b)
(c) (d)
Supplement Figure 4. Significant pathways with gene expression variations measured by microarrays. Heatmaps [10] were used to
illustrate the metabolic and signaling canonical pathways that passed at least one of the IPA statistic tests at p < 0.05 for gene expres-
sion variations in between contrasting RNA samples of HFD + UP780 vs. HFD, HFD + UP780 vs. lean control, and HFD vs. lean
control. The color gradients correspond to the –log10 transformed p-values from the IPA pathway analysis of one-tailed Fisher’s exact
tests, with yellow for the metabolic pathways and red for the signaling pathways, and black denoting missing values. A. liver meta-
bolic pathways; B, liver signaling pathways; C, WAT metabolic pathways; and D, WAT signaling pathways. C is an exception in that
the cutoff value for log2 ratio was set at 0.5 instead of 0.8 when conducting the IPA pathway analysis, as described in materials and
methods.

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 48
LUP-LV
(a)
LUP-LC
(b)

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 49
LV-LC
(c)
Supplement Figure 5. Liver canonical pathway of fatty acid biosynthesis. Fatty acid biosynthesis
pathway figures for comparisons A, LUP-LV, B, LUP-LC, and C, LV-LC were overlaid with red (up-
regulation) and green (down-regulation) according to the values of log2 ratio, with color gradient denoting
the scale of up- or down-regulation. The figures were exported from the Ingenuity Pathway Analysis.
(a)

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 50
(b)
(c)
Supplement Figure 6. WAT canonical pathway of insulin receptor signaling. Insulin receptor signaling
pathway figures for comparisons A, FUP-FV, B, FUP-FC, and C, FV-FC were overlaid with red (up-regu-
lation) and green (down-regulation) according to the values of log2 ratio, with color gradient denoting the
scale of up- or down-regulation. The figures were exported from the Ingenuity Pathway Analysis.

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 51
Supplement Table 3.
FUP/FV FUP/FC FV/FC
Name Description RefSeq ID
p-value Log
Ratio Intensityp-valueLog Ratio Intensity p-value Log Ratio Intensity
Propanoate Metabolism
ACACA
acetyl-Coenzyme
A carboxylase alpha NM_133360 0.0340.83312.6560.009 −2.075.182 0.001 −1.73 11.823
ACACB
acetyl-Coenzyme
A carboxylase beta NM_133904 0.031.1649.508 0.8930.0599.449 0.036 −1.1068.344
ACAD10
acyl-Coenzyme A
dehydrogenase
family, member 10
NM_028037 0.0080.9068.3870.370.0682.183 0.003 −1.1 7.481
ACAD11
acyl-Coenzyme
A dehydrogenase
family, member 11
NM_028721 0.0090.58712.5080.3760.18513.851 0.03 −0.442 11.922
ACAD8
acyl-Coenzyme
A dehydrogenase
family, member 8
NM_025862 0.0050.5379.1940.004−0.5599.753 0
−1.097 8.657
ACADSB
acyl-Coenzyme
A dehydrogenase,
short/branched chain
NM_025826 0.0230.50512.4850.09−0.33812.823 0.002 −0.843 11.98
ACSM5
acyl-CoA synthetase
medium-chain
family member 5
NM_178758 0.0291.7816.6830.783−0.1816.864 0.019 −1.9634.901
ALDH2
aldehyde dehydrogenase
2 family (mitochondrial) NM_009656 0.0220.5338.2980.104−0.30213.448 0.003 −0.756 12.692
ALDH5A1
aldehyde dehydrogenase
5 family, member A1
(succinate-semialdehyde
dehydrogenase)
NM_172532 0.0120.80210.1080.459 −0.1810.288 0.004 −0.982 9.306
ALDH6A1 aldehyde dehydrogenase
6 family, member A1 NM_134042 0.0020.50312.5660.009−0.35912.925 0
−0.862 12.064
ALDH7A1 aldehyde dehydrogenase
7 family, member A1 NM_138600 0.0630.44812.2810.129−0.34612.627 0.006 −0.793 11.833
DHCR24
24-dehydrocholesterol
reductase NM_053272 0.012−0.7888.527 0.8690.0398.489 0.009
0.827 9.315
ECHS1
enoyl Coenzyme A
hydratase, short chain,
1, mitochondrial
NM_053119 0.0410.41113.8740.457−0.12714.001 0.014 −0.539 13.463
EHHADH
enoyl-Coenzyme A,
hydratase/3-hydroxyacyl
Coenzyme A
dehydrogenase
NM_023737 0.0440.60510.0520.570.1459.907 0.103 −0.469.447
GCDH
glutaryl-Coenzyme
A dehydrogenase NM_0010447440.0460.49110.4130.859 −0.03710.45 0.036 −0.5289.922
HIBCH
3-hydroxyisobutyryl-
Coenzyme A hydrolase NM_146108 0.0410.50912.6050.496−0.3036.948 0.017 −0.641 12.096
IVD
isovaleryl Coenzyme
A dehydrogenase NM_019826 0.0130.84713.680.052 −0.5511.655 0.001 −1.253 10.402
LDHB lactate dehydrogenase B NM_008492 0.0780.39113.6270.192−0.27812.671 0.016 −0.608 13.236
MUT
methylmalonyl
Coenzyme A mutase NM_008650 0.0070.45513.3040.255−0.0032.125 0.004 −0.52712.849
PCCB
propionyl Coenzyme A
carboxylase, beta
polypeptide
NM_025835 0.0150.85212.850.714−0.09912.95 0.009 −0.951 11.999
SUCLG2
succinate-CoA ligase,
GDP-forming,
beta subunit
NM_011507 0.0360.72910.320.106−0.32912.734 0.004 −0.77611.958
Valine, Leucine and Isoleucine Degradation
9330129D05RIK RIKEN cDNA
9330129D05 gene XM_488540 0.0031.0829.448 0.2980.26 9.188 0.011 −0.822 8.366
ACAA1B
acetyl-Coenzyme
A acyltransferase 1B NM_130864 0.138−0.28513.1070.0090.61712.489 0.001
0.902 13.391
ACAD10
acyl-Coenzyme A
dehydrogenase family,
member 10
NM_028037 0.0080.9068.3870.370.0682.183 0.003 −1.1 7.481

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 52
Continued
ACAD11
acyl-Coenzyme A
dehydrogenase family,
member 11
NM_028721 0.0090.58712.5080.3760.185 13.851 0.03 −0.442 11.922
ACAD8
acyl-Coenzyme A
dehydrogenase family,
member 8
NM_025862 0.0050.5379.1940.004−0.559 9.753 0 −1.097 8.657
ACADSB
acyl-Coenzyme A
dehydrogenase,
short/branched chain
NM_025826 0.0230.50512.4850.09−0.338 12.823 0.002 −0.84311.98
ALDH2
aldehyde dehydrogenase
2 family (mitochondrial) NM_009656 0.0220.5338.2980.104−0.302 13.448 0.003 −0.756 12.692
ALDH5A1
aldehyde dehydrogenase
5 family, member A1
(succinate-semialdehyde
dehydrogenase)
NM_172532 0.0120.80210.108 0.459−0.18 10.288 0.004 −0.982 9.306
ALDH6A1 aldehyde dehydrogenase
6 family, member A1 NM_134042 0.0020.50312.5660.009−0.359 12.925 0 −0.86212.064
ALDH7A1 aldehyde dehydrogenase
7 family, member A1 NM_138600 0.0630.44812.2810.129−0.346 12.627 0.006 −0.793 11.833
BCAT1
branched chain
aminotransferase 1,
cytosolic
NM_0010244680.448 −0.6187.920.018 0.877 3.754 0.007 1.091 4.845
BCAT2
branched chain
aminotransferase 2,
mitochondrial
NM_009737 0.10.5138.9350.339−0.276 9.211 0.024 −0.789 8.422
BCKDHA
branched chain keto
acid dehydrogenase
E1, alpha polypeptide
NM_007533 0.0370.65513.0870.968−0.01 13.097 0.035 −0.666 12.431
DBT
dihydrolipoamide
branched chain
transacylase E2
NM_010022 0.0240.64110.5120.138−0.369 10.882 0.003 −1.01 9.871
ECHS1
enoyl Coenzyme A
hydratase, short
chain, 1, mitochondrial
NM_053119 0.0410.41113.8740.457−0.127 14.001 0.014 −0.539 13.463
EHHADH
enoyl-Coenzyme A,
hydratase/3-hydroxyacyl
Coenzyme A
dehydrogenase
NM_023737 0.0440.60510.0520.570.145 9.907 0.103 −0.469.447
GCDH
glutaryl-Coenzyme A
dehydrogenase NM_0010447440.0460.49110.413 0.859 −0.037 10.45 0.036 −0.528 9.922
HIBCH
3-hydroxyisobutyryl-
Coenzyme A hydrolase NM_146108 0.0410.50912.6050.496−0.303 6.948 0.017 −0.641 12.096
HMGCS1
3-hydroxy-3-
methylglutaryl-
Coenzyme A synthase
1 (soluble)
NM_145942 0.2530.25612.310.0130.699 11.61 0.023 0.65914.896
HMGCS2
3-hydroxy-3-
methylglutaryl-
Coenzyme A synthase
2 (mitochondrial)
NM_008256 0.0061.25711.845 0.0310.868 10.978 0.258 −0.3910.588
IVD
isovaleryl Coenzyme A
dehydrogenase NM_019826 0.0130.84713.68 0.052 −0.55 11.655 0.001 −1.25310.402
MCCC1
methylcrotonoyl-
Coenzyme A
carboxylase 1 (alpha)
NM_023644 0.0270.44413.7010.321−0.168 13.868 0.007 −0.612 13.256
MCCC2
methylcrotonoyl-
Coenzyme A
carboxylase 2 (beta)
NM_030026 0.0090.52112.30.096−0.275 12.575 0.001 −0.796 11.779
MUT
methylmalonyl
Coenzyme A mutase NM_008650 0.0070.45513.3040.255−0.003 2.125 0.004 −0.527 12.849
PCCB
propionyl Coenzyme
A carboxylase,
beta polypeptide
NM_025835 0.0150.85212.850.714 −0.099 12.95 0.009 −0.951 11.999
Beta-Alanine Metabolism
9330129D05RIK RIKEN cDNA
9330129D05 gene XM_488540 0.0031.0829.4480.2980.26 9.188 0.011 −0.822 8.366

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 53
Continued
ACAD10
acyl-Coenzyme A
dehydrogenase
family, member 10
NM_028037 0.0080.9068.3870.370.068 2.183 0.003 −1.1 7.481
ACAD11
acyl-Coenzyme A
dehydrogenase
family, member 11
NM_028721 0.0090.58712.5080.3760.185 13.851 0.03 −0.44211.922
ACAD8
acyl-Coenzyme A
dehydrogenase
family, member 8
NM_025862 0.0050.5379.1940.004−0.559 9.753 0 −1.0978.657
ACADSB
acyl-Coenzyme A
dehydrogenase,
short/branched chain
NM_025826 0.0230.50512.4850.09−0.338 12.823 0.002 −0.84311.98
ALDH2
aldehyde dehydrogenase
2 family (mitochondrial) NM_009656 0.0220.5338.2980.104−0.302 13.448 0.003 −0.756 12.692
ALDH5A1
aldehyde dehydrogenase
5 family,member A1
(succinate-semialdehyde
dehydrogenase)
NM_172532 0.0120.80210.1080.459−0.18 10.288 0.004 −0.9829.306
ALDH6A1 aldehyde dehydrogenase
6 family, member A1 NM_134042 0.0020.50312.5660.009−0.359 12.925 0 −0.862 12.064
ALDH7A1 aldehyde dehydrogenase
7 family, member A1 NM_138600 0.0630.44812.2810.129−0.346 12.627 0.006 −0.793 11.833
AOC3
amine oxidase, copper
containing 3 (vascular
adhesion protein 1)
NM_009675 0.0050.5314.4160.186−0.191 14.607 0.001 −0.721 13.886
DPYD
dihydropyrimidine
dehydrogenase NM_170778 0.0130.6379.480.055−0.441 9.921 0.001
−1.078 8.843
ECHS1
enoyl Coenzyme A
hydratase, short chain,
1, mitochondrial
NM_053119 0.0410.41113.8740.457−0.127 14.001 0.014 −0.539 13.463
EHHADH
enoyl-Coenzyme A,
hydratase/3-hydroxyacyl
Coenzyme A
dehydrogenase
NM_023737 0.0440.60510.0520.570.145 9.907 0.103 −0.46 9.447
GCDH
glutaryl-Coenzyme
A dehydrogenase NM_0010447440.0460.49110.4130.859 −0.037 10.45 0.036 −0.5289.922
HIBCH
3-hydroxyisobutyryl-
Coenzyme
A hydrolase
NM_146108 0.0410.50912.6050.496−0.303 6.948 0.017 −0.641 12.096
IVD
isovaleryl Coenzyme
A dehydrogenase NM_019826 0.0130.84713.680.052−0.55 11.655 0.001 −1.253 10.402
SMS spermine synthase NM_009214 0.01−0.4417.060.0120.423 6.637 0 0.8647.501
Glycosphingolipid Biosynthesis—Ganmglioseries
B4GALNT1
beta-1,4-N-acetyl-
galactosaminyl
transferase 1
NM_008080 0.023−0.8268.1620.1380.472 7.69 0.003 1.2998.988
CHI3L3 chitinase 3-like 3 NM_009892 0.047−0.997 6.0540.0780.85 5.203 0.003 1.847 7.05
DBT
dihydrolipoamide
branched chain
transacylase E2
NM_010022 0.0240.64110.5120.138−0.369 10.882 0.003 −1.019.871
GLB1 galactosidase, beta 1 AW553762 0.044 0.9177.970.0040.282 10.92 0.001 0.36911.288
GLB1L
galactosidase, beta
1-like BB207162 0.0050.6368.0140.207−0.019 2.343 0.006 −0.6157.378
GLB1L2
galactosidase, beta
1-like 2 NM_153803 0.0280.50814.0960.033−0.47 13.134 0.002
−0.879 12.256
ST3GAL2
ST3 beta-galactoside
alpha-2,3-
sialyltransferase 2
NM_009179 0.0040.9647.7150.099 −0.416 7.643 0.002 −1.0516.751
ST3GAL4
ST3 beta-galactoside
alpha-2,3-
sialyltransferase 4
NM_009178 0.0061.0379.9680.253 −0.011 2.324 0.003 −1.2348.931

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 54
Continued
ST6GALNAC4
ST6 (alpha-N-acetyl-
neuraminyl-2, 3-beta-
galactosyl-1,3)-N-
acetylgalactosaminide
alpha-2,6-sialyltransferase 4
NM_011373 0.005−0.8425.3090.0590.467 4.842 0.001 1.309 6.151
ST8SIA4
ST8 alpha-N-acetyl-
neuraminide alpha-2,
8-sialyltransferase 4
NM_009183 0.049−1.5292.7590.640.31 2.449 0.025 1.839 4.287
Sphingolipid Metabolism
ASAH2
N-acylsphingosine
amidohydrolase
(non-lysosomal
ceramidase) 2
NM_018830 0.0020.5649.0840.039−0.286 9.37 0 −0.8498.52
CERK
(includes EG:64781) ceramide kinase NM_145475 0.153−0.4869.4490.0590.686 8.763 0.007
1.172 9.935
GALC galactosylceramidase NM_008079 0.198−0.39110.185 0.0021.087 4.748 0.002 1.059 5.806
GLA galactosidase, alpha NM_013463 0.045−1.008 8.5 0.0510.969 7.53 0.002 1.977 9.508
GLB1 galactosidase, beta 1 −−− 0.0440.9177.970.0040.282 10.92 0.001 0.36911.288
GLB1L galactosidase, beta 1-like −−− 0.0050.6368.0140.207−0.019 2.343 0.006 −0.615 7.378
GLB1L2 galactosidase, beta 1-like 2 NM_153803 0.0280.50814.0960.033−0.47 13.134 0.002 −0.879 12.256
KDSR
3-ketodihydrosphingosine
reductase NM_027534 0.0040.769.1150.093−0.337 9.452 0.001
−1.097 8.355
PPAP2A
phosphatidic
acid phosphatase
type 2A
NM_008247 0.154−0.30811.420.3090.21 11.209 0.033 0.51811.728
SPHK1 sphingosine kinase 1 NM_011451 0.017−1.1734.7660.1130.668 4.098 0.002 1.841 5.939
SULF1 sulfatase 1 NM_172294 0.0740.66111.0970.284−0.315 2.943 0.049 −0.753 10.436
SULF2 sulfatase 2 NM_028072 0.0020.6612.8890.5450.245 8.922 0.003 −0.627 12.229
UGCG
UDP-glucose ceramide
glucosyltransferase NM_011673 0.0010.7447.7380.1210.247 7.49 0.01 −0.3686.274
VNN1 vanin 1 NM_011704 0.0030.913 9.7470.0190.614 9.133 0.173 −0.3 8.834
VNN2 vanin 2 NM_011979 0.0051.42910.815 0.745 −0.118 10.932 0.004 −1.547 9.386
Nicotine and Nicotinamide Metabolism
ACVR2A activin A receptor, type IIA NM_007396 0.06−0.3955.9980.1090.322 5.676 0.005 0.717 6.393
AKT2
v-akt murine thymoma viral
oncogene homolog 2 NM_0011102080.020.69211.060.4890.164 10.896 0.016 −0.43913
ARAF
v-raf murine sarcoma 3611
viral oncogene homolog NM_009703 0.0380.37610.450.2580.245 11.406 0.02
−0.912 3.647
BST1
bone marrow stromal cell
antigen 1 NM_009763 0.186−0.4668.1010.320.338 7.763 0.041
0.804 8.566
CD38 CD38 molecule NM_007646 0.0021.1627.2850.035 −0.377 10.359 0 −1.043 9.315
CDC2
cell division cycle 2, G1 to
S and G2 to M NM_007659 0.013−1.395 8.3420.021.253 7.088 0 2.648 9.736
CDK6 cyclin-dependent kinase 6 NM_009873 0.024−0.7629.0290.0930.629 7.834 0.003
1.211 9.791
CDK7 cyclin-dependent kinase 7 NM_009874 0.043−0.5915.7520.161−0.283 6.617 0.023 −0.533 6.084
CSNK1D casein kinase 1, delta NM_027874 0.0360.59310.450.253−0.043 2.526 0.026 −0.345 9.897
EIF2AK2
eukaryotic translation
initiation actor 2-alpha
kinase 2
NM_011163 0.0340.586.3760.2610.163 6.524 0.088 −0.433 5.796
ENPP1
ectonucleotide
pyrophosphatase/
phosphodiesterase 1
NM_008813 0.046−1.4055.350.185 0.845 4.505 0.007 2.25 6.755

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 55
Continued
ENPP2
ectonucleotide
pyrophosphatase/
phosphodiesterase
2 (autotaxin)
NM_015744 0 0.63413.7330 −0.484 5.976 0 −1.215 13.099
ENPP3
ectonucleotide
pyrophosphatase/
phosphodiesterase 3
NM_134005 0.0960.4727.5010.253−0.175 8.227 0.031 −0.667 7.029
ENPP5
Ectonucleotide
pyrophosphatase/
phosphodiesterase 5
(putative function)
NM_032003 0.020.66311.6210.352−0.216 11.837 0.006 −0.879 10.958
GRK5
G protein-coupled receptor
kinase 5 NM_018869 0.166−0.24210.3660.0280.436 9.93 0.004 0.67810.608
IRAK1
interleukin-1
receptor-associated
kinase 1
NM_008363 0.0080.41711.9850.062−0.131 8.168 0.003 −0.53 11.568
MAPK9
mitogen-activated
protein kinase 9 NM_016961 0.060.2157.4490.012−0.33 7.779 0.001 −0.545 7.234
NAMPT
nicotinamide
phosphoribosyltransferase NM_021524 0.0260.2077.3550.001−0.512 10.566 0 −0.529 7.147
NEK2
NIMA (never
in mitosis gene a)
related kinase 2
−−− 0.2530.0122.1350.0511.088 3.839 0.024 1.33 5.169
NMNAT1
nicotinamide nucleotide
adenylyltransferase 1 NM_133435 0.039−0.2986.9040.0110.409 6.495 0.001 0.708 7.203
NMNAT3
(includes EG:349565)
nicotinamide nucleotide
adenylyltransferase 3 NM_144533 0.801−0.0516.6030.025−0.574 7.177 0.035 −0.522 6.654
NNT
nicotinamide nucleotide
transhydrogenase NM_008710 0.0860.2519.1470.002−0.481 7.964 0 −0.66 7.304
NT5E 5’-nucleotidase, ecto (CD73) NM_011851 0.0021.2335.6670.003 −1.063 6.73 0 −2.296 4.434
PAK1
p21/Cdc42/Rac1-activated
kinase 1 (STE20 homolog,
yeast)
NM_011035 0.036−0.9627.9840.3010.477 7.838 0.013 1.4469.283
PCTK3 PCTAIRE protein kinase 3 NM_008795 0.052−1.766 6.5420.001 3.965 2.577 0 5.738.308
PIM1 pim-1 oncogene NM_008842 0.032−1.33.5450.4590.18 8.558 0.06 1.086 4.845
PRKAA1
protein kinase,
AMP-activated,
alpha 1 catalytic
subunit
NM_0010133670.0090.4086.520.001 −0.631 7.151 0 −1.039 6.112
PRKCD protein kinase C, delta NM_011103 0.15−0.27311.2390.0330.451 10.788 0.004 0.724 11.512
PRKCH protein kinase C, eta NM_008856 0.087−0.743 10.472 0.0270.997 7.892 0.003 1.594 9.486
PRPF4B
PRP4 pre-mRNA
processing factor
4 homolog B (yeast)
NM_013830 0.0080.3458.0060.071−0.264 9.994 0.002 −0.563 8.844
VNN1 vanin 1 NM_011704 0.0030.913 9.7470.0190.614 9.133 0.173 −0.38.834
VNN2 vanin 2 NM_011979 0.0051.42910.815 0.745 −0.118 10.932 0.004 −1.547 9.386
Fatty Acid Biosynthesis
ACACA
acetyl-Coenzyme
A carboxylase alpha NM_133360 0.0340.83312.656 0.009−2.07 5.182 0.001 −1.73 11.823
ACACB
acetyl-Coenzyme
A carboxylase beta NM_133904 0.031.164 9.5080.8930.059 9.449 0.036 −1.106 8.344
FASN fatty acid synthase NM_007988 0.2620.18514.6060.017−0.48 15.086 0.004 −0.665 14.421
MCCC2
methylcrotonoyl-Coenzyme
A carboxylase 2 (beta) NM_030026 0.0090.52112.30.096−0.275 12.575 0.001 −0.796 11.779
PCCB
propionyl Coenzyme A
carboxylase, beta
polypeptide
NM_025835 0.0150.85212.850.714−0.099 12.95 0.009 −0.951 11.999
Glycerolipid Metabolism
ADHFE1
alcohol dehydrogenase,
iron containing, 1 NM_175236 0.0240.50613.3250.188−0.253 13.578 0.004 −0.76 12.819

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 56
Continued
AGPAT5
1-acylglycerol-3-
phosphate
O-acyltransferase 5
(lysophosphatidic acid
acyltransferase, epsilon)
NM_026792 0.006−0.45310.340.2430.2 9.39 0.002 0.57410.793
AKR1B10
aldo-keto reductase family
1, member B10
(aldose reductase)
NM_172398 0.026−0.3411.3590.0230.349 11.01 0.001 0.69 11.699
ALDH2
aldehyde dehydrogenase 2
family (mitochondrial) NM_009656 0.0220.5338.2980.104−0.302 13.448 0.003 −0.75612.692
ALDH5A1
aldehyde dehydrogenase 5
family, member A1
(succinate-semialdehyde
dehydrogenase)
NM_172532 0.0120.80210.1080.459−0.18 10.288 0.004 −0.982 9.306
ALDH7A1
aldehyde dehydrogenase 7
family, member A1 NM_138600 0.0630.44812.2810.129−0.346 12.627 0.006 −0.793 11.833
APOC2 apolipoprotein C-II NM_009695 0.187−0.449.3160.0730.639 8.677 0.01 1.089.756
CERK
(includes EG:64781) ceramide kinase NM_145475 0.153−0.4869.4490.0590.686 8.763 0.007
1.172 9.935
DAGLB diacylglycerol lipase, beta NM_144915 0.054−0.52710.1140.080.466 9.649 0.004 0.992 10.641
DGKZ
diacylglycerol kinase,
zeta 104 kDa NM_138306 0.106−0.39911.3970.0170.6 7.504 0.004
0.841 8.345
GK glycerol kinase NM_008194 0.03−0.8977.8210.5640.193 6.204 0.018 1.006 7.21
GLA galactosidase, alpha NM_013463 0.045−1.0088.5 0.0510.969 7.53 0.002 1.9779.508
GLB1 galactosidase, beta 1 −−− 0.0440.9177.970.0040.282 10.92 0.001 0.36911.288
GLB1L
galactosidase, beta
1-like −−− 0.0050.6368.0140.207−0.019 2.343 0.006 −0.615 7.378
GLB1L2
galactosidase, beta
1-like 2 NM_153803 0.0280.50814.0960.033−0.47 13.134 0.002
−0.879 12.256
GLYCTK glycerate kinase NM_0010395860.155−0.6223.750.0690.844 2.906 0.008 1.4664.371
GPAM
glycerol-3-phosphate
acyltransferase,
mitochondrial
NM_008149 0.0190.9779.2150.15−0.377 13.572 0.005 −1.3268.238
LIPA
lipase A, lysosomal acid,
cholesterol esterase
(Wolman disease)
NM_0011111000.044 −0.9719.896 0.027 0.828 12.45 0.002 1.49813.949
LIPF lipase, gastric NM_026334 0.21−1.319 8.1530.013.418 4.734 0.002 4.7389.472
MGLL monoglyceride lipase NM_011844 0.0030.27414.6770.0190.185 14.492 0.017 0.819 5.255
MOGAT1
monoacylglycerol
O-acyltransferase 1 NM_026713 0.0451.2310.980.274 −0.589 11.569 0.009 −1.819 9.75
PNPLA3
patatin-like phospholipase
domain
containing 3
NM_054088 0.3090.3519.1540.157−0.51 9.663 0.033 −0.861 8.803
PPAP2A
phosphatidic
acid phosphatase
type 2A
NM_008247 0.154−0.30811.420.3090.21 11.209 0.033 0.51811.728
SPHK1 sphingosine kinase 1 NM_011451 0.017−1.1734.7660.1130.668 4.098 0.002 1.8415.939
TCAG7.1260
similar to aldo-keto
reductase
family 1, member B10
NM_008012 0.059−0.59312.1790.5990.143 12.036 0.027 0.736 12.772
Glutathione Metabolism
G6PD2
glucose-6-phosphate
dehydrogenase 2 NM_008062 0.0860.20811.5920.0010.59 11.002 0.009 0.38111.384
GCLM
glutamate-cysteine ligase,
modifier subunit NM_008129 0.138−0.358 10.5770.366 −0.214 7.458 0.04 0.546 10.935
GGT6 gamma-glutamyltransferase 6 NM_027819 0.002−1.324.6 0.1230.479 4.12 0 1.799 5.919
GPX3
glutathione peroxidase 3
(plasma) NM_0010839290.0080.69215.37 0.063 −0.41 15.78 0.001
−1.102 14.677
GSTA3 glutathione S-transferase A3 NM_0010773530.0610.95311.4150.127 −0.725 9.233 0.006 −1.656 7.577

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 57
Continued
GSTA4 glutathione S-transferase A4 NM_0103570.040.85311.3860.122−0.589 11.975 0.004 −1.441 10.533
GSTO1
glutathione S-transferase
omega 1 NM_0103620.102−0.28310.549 0.0060.46312.792 0.001 0.67313.464
GSTT1
glutathione S-transferase
theta 1 NM_0081850.0130.59 12.7910.026−0.502 13.293 0.001 −1.09212.201
GSTT2
glutathione S-transferase
theta 2 NM_0103610.006 0.68311.146 0.63 −0.086 11.232 0.004 −0.77 10.463
GSTT3
glutathione S-transferase,
theta 3 NM_1339940.022 0.8628.1330.007 −1.124 9.257 0 −1.987 7.271
H6PD
hexose-6-phosphate
dehydrogenase (glucose
1-dehydrogenase)
NM_1733710.0020.68814.002 0.939 −0.011 14.013 0.002 −0.69913.314
IDH2
isocitrate dehydrogenase 2
(NADP+), mitochondrial NM_1730110.0140.50513.0760.9510.01 13.067 0.016 −0.49612.571
LNPEP
leucyl/cystinyl
aminopeptidase NM_1728270.002 0.53911.7720.05 −0.046 2.178 0 −0.78711.232
LTC4S leukotriene C4 synthase NM_0085210.665−0.04214.4760 0.74813.728 0 0.79 14.517
MGST2
microsomal glutathione
S-transferase 2 NM_1749950.043−0.45710.7390.3270.19210.547 0.011 0.64911.196
PGDS
prostaglandin D2 synthase,
hematopoietic NM_0194550.112−1.7157.268 0.1031.77 5.498 0.009 3.4858.984
RAB15
RAB15, member RAS
onocogene family NM_1340500.18 −0.6697.353 0.106 0.8376.516 0.014 1.507 8.023
TRHDE
thyrotropin-releasing
hormone degrading
enzyme
NM_1462410.1180.9914.864 0.058 −1.276.134 0.006 −2.261 3.873
Lysine Biosynthesis
AASDHPPT
aminoadipate-semialdehyde
dehydrogenase-
phosphopantetheinyl
transferase
NM_0262760.0170.56 7.3370.036−0.463 7.8 0.001 −1.024 6.777
VNN1 vanin 1 NM_0117040.0030.9139.747 0.019 0.6149.133 0.173 −0.3 8.834
VNN2 vanin 2 NM_0119790.0051.42910.8150.745 −0.118 10.932 0.004 −1.547 9.386
Pyruvate Metabolism
ACACA
acetyl-Coenzyme
A carboxylase alpha NM_1333600.034 0.83312.6560.009−2.075.182 0.001 −1.73 11.823
ACACB
acetyl-Coenzyme
A carboxylase beta NM_1339040.03 1.1649.5080.893 0.0599.449 0.036 −1.106 8.344
ACSM5
acyl-CoA synthetase
medium-chain
family member 5
NM_1787580.0291.7816.6830.783 −0.181 6.864 0.019 −1.963 4.901
AKR1B10
aldo-keto reductase
family 1, member B10
(aldose reductase)
NM_1723980.026−0.3411.3590.023 0.34911.01 0.001 0.69 11.699
ALDH2
aldehyde dehydrogenase 2
family (mitochondrial) NM_0096560.0220.5338.2980.104 −0.302 13.448 0.003 −0.75612.692
ALDH5A1
aldehyde dehydrogenase 5
family, member A1
(succinate-semialdehyde
dehydrogenase)
NM_1725320.0120.80210.1080.459−0.1810.288 0.004 −0.982 9.306
ALDH7A1
aldehyde dehydrogenase
7 family, member A1 NM_1386000.0630.44812.281 0.129 −0.346 12.627 0.006 −0.79311.833
BCKDHA
branched chain keto acid
dehydrogenase E1, alpha
polypeptide
NM_0075330.0370.65513.087 0.968−0.0113.097 0.035 −0.66612.431
LDHB lactate dehydrogenase B NM_0084920.0780.39113.6270.192−0.278 12.671 0.016 −0.60813.236
LDHD lactate dehydrogenase D NM_0275700.0330.88 9.4910.574−0.179 9.868 0.055 −0.7628.611
NKD1
naked cuticle homolog 1
(Drosophila) NM_0272800.147−0.3838.007 0.177 0.3536.959 0.021 0.7038.389
NUDT7
nudix (nucleoside
diphosphate linked
moiety X)-type motif 7
NM_0244370.001−0.56811.7350.0580.31312.288 0 0.77612.302

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 58
Continued
PC pyruvate carboxylase NM_008797 0.0530.35514.5850.334−0.157 14.741 0.013 −0.511 14.23
PCK1
phosphoenolpyruvate
carboxykinase 1 (soluble) NM_011044 0.0022.193 12.8270.7830.181 12.921 0.002 −2.229 10.633
PDHA1
(includes EG:5160)
pyruvate dehydrogenase
(lipoamide) alpha 1 NM_008810 0.0120.25514.6660.003−0.349 15.014 0 −0.603 14.411
PDHB
pyruvate dehydrogenase
(lipoamide) beta NM_024221 0.3060.14914.0830.019−0.774 10.036 0.006 −0.54113.934
RWDD2B RWD domain containing 2B NM_016924 0.014−0.67.6270.7470.061 7.566 0.009 0.661 8.227
TCAG7.1260
similar to aldo-keto
reductase family 1,
member B10
NM_008012 0.059−0.59312.1790.5990.143 12.036 0.027 0.736 12.772
Aminosugars Metabolism
CHI3L3 chitinase 3-like 3 NM_009892 0.047−0.9976.054 0.0780.85 5.203 0.003 1.8477.05
CMAH
cytidine monophosphate-
N-acetylneuraminic acid
hydroxylase(CMP-N-
acetylneuraminate
monooxygenase)
pseudogene
NM_0011111100.0380.5635.526 0.181 −0.07 3.162 0.13 −0.3754.964
CMAS
cytidine monophosphate
N-acetylneuraminic acid
synthetase
NM_009908 0.102−0.22311.7270.0340.314 11.413 0.003 0.53711.95
CYB561 cytochrome b-561 BE133856 0.2310.0522.1780.1460.39 9.951 0.049 0.57110.522
HK1 hexokinase 1 NM_010438 0.0420.8137.6970.1950.464 7.233 0.316 −0.3496.884
HK2 hexokinase 2 NM_013820 0.310.19511.4540.024−0.519 11.973 0.006 −0.71311.259
HK3 hexokinase 3 (white cell) NM_0010332450.03−0.9668.121 0.017 1.122 6.999 0.001 2.0879.086
NANS
N-acetylneuraminic
acid synthase
(sialic acid synthase)
NM_053179 0.002−0.6639.190.0250.229 11.614 0 0.545 12.159
PDE1A
phosphodiesterase 1A,
calmodulin-dependent NM_0010099780.003 1.2398.6990.059 −0.608 9.306 0 −1.847 7.46
PDE2A
phosphodiesterase 2A,
cGMP-stimulated NM_0010085480.148 −0.25210.0920.0040.683 9.41 0.001
0.935 10.345
PDE3B
phosphodiesterase 3B,
cGMP-inhibited NM_011055 0.0030.49113.1190.129−0.179 13.298 0 −0.6712.628
PDE4B
phosphodiesterase 4B,
cAMP-specific
(phosphodiesterase E4
dunce homolog, Drosophila)
NM_019840 0 1.1048.990.0010.883 8.107 0.222 −0.2227.885
PDE7A phosphodiesterase 7A NM_0011227590.14−0.4368.998 0.003 1.237 8.55 0.001 1.448 9.997
PDE7B phosphodiesterase 7B NM_013875 0.11−0.6729.4160.1130.666 8.75 0.009 1.339 10.088
PDE8B phosphodiesterase 8B NM_172263 0.043−1.0833.1460.8030.111 3.035 0.03 1.194 4.229
PGM3 phosphoglucomutase 3 NM_028352 0.1350.358.5210.451−0.164 8.685 0.044 −0.5148.172
RENBP renin binding protein NM_023132 0.019−0.63210.6410.0290.571 10.07 0.001
1.204 11.273
UAP1
UDP-N-acteylglucosamine
pyrophosphorylase 1 NM_133806 0.0060.43410.8550.123−0.229 9.853 0.002 −0.54710.421
Phenylalanine Metabolism
ALDH2
aldehyde dehydrogenase 2
family (mitochondrial) NM_009656 0.0220.5338.2980.104−0.302 13.448 0.003 −0.75612.692
ALDH3B1
aldehyde dehydrogenase 3
family, member B1 NM_026316 0.017−0.567.8480.0460.431 7.417 0.001
0.992 8.409
AOC3
amine oxidase, copper
containing 3 (vascular
adhesion protein 1)
NM_009675 0.0050.5314.4160.186−0.191 14.607 0.001 −0.72113.886
DBT
dihydrolipoamide branched
chain transacylase E2 NM_010022 0.0240.64110.5120.138−0.369 10.882 0.003 −1.01 9.871

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 59
Continued
DHCR24
24-dehydrocholesterol
reductase NM_053272 0.012−0.7888.5270.8690.039 8.489 0.009 0.827 9.315
GOT1
glutamic-oxaloacetic
transaminase 1, soluble
(aspartate aminotransferase 1)
NM_010324 0.798−0.0529.4890.0380.51 8.978 0.026 0.5639.541
MAOA monoamine oxidase A NM_173740 0.01−0.52312.2620.582 −0.229 7.565 0.008 0.559 12.784
MAOB monoamine oxidase B NM_172778 0.0380.46312.20.035−0.473 12.673 0.002 −0.93611.737
MIF
macrophage migration
inhibitory factor
(glycosylation-inhibiting
factor)
NM_010798 0.049−0.25613.2820.0370.277 13.005 0.002 0.53413.539
Tyrosine Metabolism
ADHFE1
alcohol dehydrogenase, iron
containing, 1 NM_175236 0.0240.50613.3250.188−0.253 13.578 0.004 −0.76 12.819
ALDH2
aldehyde dehydrogenase
2 family (mitochondrial) NM_009656 0.0220.5338.2980.104−0.302 13.448 0.003 −0.75612.692
ALDH3B1
aldehyde dehydrogenase
3 family, member B1 NM_026316 0.017−0.567.8480.0460.431 7.417 0.001
0.992 8.409
AOC3
amine oxidase, copper
containing 3 (vascular
adhesion protein 1)
NM_009675 0.0050.5314.4160.186−0.191 14.607 0.001 −0.72113.886
BCKDHA
branched chain keto acid
dehydrogenase
E1, alpha polypeptide
NM_007533 0.0370.65513.0870.968−0.01 13.097 0.035 −0.66612.431
DBT
dihydrolipoamide branched
chain transacylase E2 NM_010022 0.0240.64110.5120.138−0.369 10.882 0.003 −1.01 9.871
FRRS1 ferric-chelate reductase 1 NM_0011134780.039−0.5429.8680.0380.545 9.323 0.002 1.087 10.41
GOT1
glutamic-oxaloacetic
transaminase 1, soluble
(aspartate aminotransferase 1)
NM_010324 0.798−0.0529.4890.0380.51 8.978 0.026 0.5639.541
MAOA monoamine oxidase A NM_173740 0.01−0.52312.2620.582 −0.229 7.565 0.008 0.559 12.784
MAOB monoamine oxidase B NM_172778 0.0380.46312.20.035−0.473 12.673 0.002 −0.93611.737
MIF
macrophage migration
inhibitory factor
(glycosylation-inhibiting
factor)
NM_010798 0.049−0.25613.2820.0370.277 13.005 0.002 0.53413.539
Histidine Metabolism
ALDH2
aldehyde dehydrogenase
2 family (mitochondrial) NM_009656 0.0220.5338.2980.104−0.302 13.448 0.003 −0.75612.692
ALDH3B1 aldehyde dehydrogenase
3 family, member B1 NM_026316 0.017−0.567.8480.0460.431 7.417 0.001
0.992 8.409
ALDH5A1
aldehyde dehydrogenase
5 family, member A1
(succinate-semialdehyde
dehydrogenase)
NM_172532 0.0120.80210.1080.459−0.18 10.288 0.004 −0.9829.306
ALDH7A1 aldehyde dehydrogenase
7 family, member A1 NM_138600 0.0630.44812.2810.129−0.346 12.627 0.006 −0.79311.833
AOC3
amine oxidase, copper
containing 3 (vascular
adhesion protein 1)
NM_009675 0.0050.5314.4160.186−0.191 14.607 0.001 −0.72113.886
DBT
dihydrolipoamide branched
chain transacylase E2 NM_010022 0.0240.64110.5120.138−0.369 10.882 0.003 −1.019.871
HARS2
histidyl-tRNA synthetase 2,
mitochondrial (putative) NM_080636 0.0140.569.2060.5220.12 5.406 0.02 −0.5168.646
HNMT
histamine
N-methyltransferase NM_080462 0.0180.45211.0340.211−0.199 11.233 0.003 −0.65110.582
MAOA monoamine oxidase A NM_173740 0.01−0.52312.2620.582 −0.229 7.565 0.008 0.559 12.784
MAOB monoamine oxidase B NM_172778 0.0380.46312.20.035−0.473 12.673 0.002 −0.93611.737
PRPS1
phosphoribosyl
pyrophosphate
synthetase 1
NM_021463 0.038−0.47213.710.0050.76 12.225 0 1.18513.41

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 60
Continued
Galactose Metabolism
AKR1B10
aldo-keto reductase
family 1, member B10
(aldose reductase)
NM_172398 0.026−0.3411.3590.0230.34911.01 0.001 0.69 11.699
GAA
glucosidase, alpha; acid
(Pompe disease, glycogen
storage disease type II)
NM_008064 0.0030.66810.9840.3950.13310.851 0.006 −0.318 9.011
GLA galactosidase, alpha NM_013463 0.045−1.0088.50.051 0.9697.53 0.002 1.977 9.508
GLB1 galactosidase, beta 1 AW553762 0.0440.9177.970.0040.28210.92 0.001 0.369 11.288
GLB1L galactosidase, beta 1-like BB207162 0.0050.6368.0140.207−0.0192.343 0.006 −0.615 7.378
GLB1L2 galactosidase, beta 1-like 2 NM_153803 0.0280.50814.0960.033−0.4713.134 0.002 −0.879 12.256
HK1 hexokinase 1 NM_010438 0.0420.8137.6970.1950.4647.233 0.316 −0.349 6.884
HK2 hexokinase 2 NM_013820 0.310.19511.4540.024−0.51911.973 0.006 −0.713 11.259
HK3 hexokinase 3 (white cell) NM_0010332450.03−0.966 8.1210.017 1.1226.999 0.001 2.087 9.086
PFKM phosphofructokinase,
muscle NM_021514 0.0310.4979.3840.311−0.1989.582 0.007 −0.694 8.888
PGM1 phosphoglucomutase 1 NM_025700 0.070.34613.5570.353−0.1613.716 0.018 −0.506 13.21
PGM3 phosphoglucomutase 3 NM_028352 0.1350.358.5210.451−0.1648.685 0.044 −0.514 8.172
TCAG7.1260
similar to aldo-keto
reductase family 1,
member B10
NM_008012 0.059−0.59312.1790.5990.14312.036 0.027 0.736 12.772
UGP2 UDP-glucose
pyrophosphorylase 2 NM_139297 0.0090.32513.3740.002−0.46811.745 0 −0.747 10.998
Fatty Acid Metabolism
9330129D05RIK RIKEN cDNA
9330129D05 gene XM_488540 0.0031.0829.4480.2980.269.188 0.011 −0.822 8.366
ACAA1B acetyl-Coenzyme
A acyltransferase 1B NM_130864 0.138−0.28513.1070.0090.61712.489 0.001 0.902 13.391
ACAD10
acyl-Coenzyme A
dehydrogenase
family, member 10
NM_028037 0.0080.9068.3870.370.0682.183 0.003 −1.1 7.481
ACAD11
acyl-Coenzyme A
dehydrogenase
family, member 11
NM_028721 0.0090.58712.5080.3760.18513.851 0.03 −0.442 11.922
ACAD8
acyl-Coenzyme A
dehydrogenase
family, member 8
NM_025862 0.0050.5379.1940.004−0.5599.753 0 −1.097 8.657
ACADSB
acyl-Coenzyme A
dehydrogenase,
short/branched chain
NM_025826 0.0230.50512.4850.09−0.33812.823 0.002 −0.843 11.98
ACOX3 acyl-Coenzyme
A oxidase 3, pristanoyl NM_030721 0.3240.1827.4670.0140.5716.896 0.061 0.388 7.285
ADHFE1 alcohol dehydrogenase,
iron containing, 1 NM_175236 0.0240.50613.3250.188−0.25313.578 0.004 −0.76 12.819
ALDH2 aldehyde dehydrogenase
2 family (mitochondrial) NM_009656 0.0220.5338.2980.104−0.30213.448 0.003 −0.756 12.692
ALDH5A1
aldehyde dehydrogenase
5 family, member A1
(succinate-semialdehyde
dehydrogenase)
NM_172532 0.0120.80210.1080.459−0.1810.288 0.004 −0.982 9.306
ALDH7A1 aldehyde dehydrogenase
7 family, member A1 NM_138600 0.0630.44812.2810.129−0.34612.627 0.006 −0.793 11.833
CPT1A carnitine palmitoyltransferase
1A (liver) NM_013495 0.6090.07312.7110.0050.57812.134 0.009 0.505 12.638
CYP2C44 cytochrome P450, family 2,
subfamily c, polypeptide 44 NM_0010014460.001 −2.814 5.5490.002 2.4053.144 0 5.219 8.363
CYP2C70 cytochrome P450, family 2,
subfamily c, polypeptide 70 NM_145499 0.038−1.2892.7230.4260.4182.305 0.012 1.707 4.012

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 61
Continued
CYP2D6
cytochrome P450, family 2,
subfamily D, polypeptide 6 NM_019823 0.0011.078.3480.004−0.434 9.841 0 −0.988.862
CYP2F1
cytochrome P450, family 2,
subfamily F, polypeptide 1 NM_007817 0.4430.794.8290.003−4.431 9.26 0.001 −5.221 4.039
CYP2J2
cytochrome P450, family 2,
subfamily J, polypeptide 2 NM_010008 0.0880.2837.9180.127−0.246 8.165 0.008 −0.53 7.635
CYP4B1
cytochrome P450, family 4,
subfamily B, polypeptide 1 NM_007823 0.1080.19510.7870.0010.599 10.188 0.007 0.40410.592
ECHS1
enoyl Coenzyme A hydratase,
short chain, 1, mitochondrial NM_053119 0.0410.41113.8740.457−0.127 14.001 0.014 −0.53913.463
EHHADH
enoyl-Coenzyme A,
hydratase/3-hydroxyacyl
Coenzyme A dehydrogenase
NM_023737 0.0440.60510.0520.570.145 9.907 0.103 −0.46 9.447
GCDH
glutaryl-Coenzyme
A dehydrogenase NM_0010447440.0460.49110.4130.859 −0.037 10.45 0.036 −0.528 9.922
IVD
isovaleryl Coenzyme
A dehydrogenase NM_019826 0.0130.84713.68 0.052 −0.55 11.655 0.001 −1.253 10.402
SLC27A1
solute carrier family 27
(fatty acid transporter),
member 1
NM_011977 0.0040.813 11.7680.0160.619 11.149 0.342 −0.19410.955
Riboflavin Metabolism
ACP6
acid phosphatase 6,
lysophosphatidic NM_019800 0.5420.1288.7040.037−0.526 9.229 0.016 −0.654 8.575
ENPP1
ectonucleotide
pyrophosphatase/
phosphodiesterase 1
NM_008813 0.046−1.4055.350.1850.845 4.505 0.007 2.25 6.755
ENPP2
ectonucleotide
pyrophosphatase/
phosphodiesterase 2
(autotaxin)
NM_015744 0 0.63413.7330 −0.484 5.976 0 −1.21513.099
ENPP3
ectonucleotide
pyrophosphatase/
phosphodiesterase 3
NM_134005 0.0960.4727.5010.253−0.175 8.227 0.031 −0.667 7.029
ENPP5
ectonucleotide
pyrophosphatase/
phosphodiesterase 5
(putative function)
NM_032003 0.020.66311.6210.352−0.216 11.837 0.006 −0.87910.958
PPAPDC2
phosphatidic acid
phosphatase type 2
domain containing 2
NM_028922 0.0320.6718.2770.071−0.532 8.809 0.002 −1.203 7.606
Citrate Cycle
ACLY ATP citrate lyase NM_134037 0.3110.3812.3370.003−0.937 14.13 0.001 −1.142 12.988
ACO1 aconitase 1, soluble NM_007386 0.0140.29512.2580.008−0.335 12.593 0 −0.63 11.963
ACO2 aconitase 2, mitochondrial NM_080633 0.020.57613.9860.2540.005 2.126 0.017 −0.603 13.41
DLST
dihydrolipoamide
S-succinyltransferase
(E2 component of
2-oxo-glutarate complex)
NM_030225 0.0020.6395.3890.078−0.247 13.008 0.001 −0.676 4.75
IDH2
isocitrate dehydrogenase 2
(NADP+), mitochondrial NM_173011 0.0140.50513.0760.9510.01 13.067 0.016 −0.49612.571
PC pyruvate carboxylase NM_008797 0.0530.35514.5850.334−0.157 14.741 0.013 −0.511 14.23
PCK1
phosphoenolpyruvate
carboxykinase 1 (soluble) NM_011044 0.0022.193 12.8270.7830.181 12.921 0.002 −2.22910.633
SDHA
succinate dehydrogenase
complex, subunit A,
flavoprotein (Fp)
NM_023281 0.0030.42813.7290.069−0.199 13.927 0 −0.62613.301
SUCLG2
succinate-CoA ligase,
GDP-forming, beta subunit NM_011507 0.0360.72910.320.106−0.329 12.734 0.004 −0.776 11.958
Pantothenate and CoA Biosynthesis
BCAT1
branched chain
aminotransferase
1, cytosolic
NM_0010244680.448 −0.6187.920.0180.877 3.754 0.007 1.0914.845

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 62
Continued
BCAT2
branched chain
aminotransferase
2, mitochondrial
NM_0097370.10.5138.9350.339 −0.276 9.211 0.024 −0.789 8.422
DPYD
dihydropyrimidine
dehydrogenase NM_1707780.0130.6379.480.055 −0.441 9.921 0.001 −1.078 8.843
ENPP1
Ectonucleotide
pyrophosphatase/
phosphodiesterase 1
NM_0088130.046 −1.4055.350.1850.845 4.505 0.007 2.25 6.755
ENPP2
ectonucleotide
pyrophosphatase/
phosphodiesterase 2
(autotaxin)
NM_0157440 0.63413.7330 −0.484 5.976 0 −1.215 13.099
ENPP3
ectonucleotide
pyrophosphatase/
phosphodiesterase 3
NM_1340050.0960.4727.5010.253 −0.175 8.227 0.031 −0.667 7.029
ENPP5
ectonucleotide
pyrophosphatase/
phosphodiesterase 5
(putative function)
NM_0320030.020.66311.621 0.352 −0.216 11.837 0.006 −0.879 10.958
One Carbon Pool by Folate
EHD4 EH-domain containing 4 NM_1338380.045−0.47211.3460.3440.193 11.152 0.012 0.666 11.818
GART
phosphoribosylglycinamide
formyltransferase,
phosphoribosylglycinamide
synthetase,
phosphoribosylaminoimidazole
synthetase
NM_0102560.0260.7336.0310.158 −0.407 6.439 0.004 −1.14 5.299
MTFMT
mitochondrial
methionyl-tRNA
formyltransferase
NM_0271340.0240.535 8.7130.6440.157 4.964 0.036 −0.4798.178
MTHFD1
methylenetetrahydrofolate
dehydrogenase (NADP+
dependent) 1,
methenyltetrahydrofolate
cyclohydrolase,
formyltetrahydrofolate
synthetase
NM_1387450.1920.27710.105 0.171 −0.293 10.398 0.022 −0.571 9.827
MTHFD1L
methylenetetrahydrofolate
dehydrogenase
(NADP+ dependent) 1-like
NM_1723080.146 −0.4084.8510.240.319 4.531 0.024 0.727 5.258
MTHFD2
methylenetetrahydrofolate
dehydrogenase (NADP +
dependent) 2,
methenyltetrahydrofolate
cyclohydrolase
NM_0086380.027 −0.6168.2410.1740.329 7.912 0.004 0.945 8.857
PDPR
pyruvate dehydrogenase
phosphatase
regulatory subunit
BB667201 0.0020.44210.1520.006−0.341 10.493 0 −0.7839.71
TYMS thymidylate synthetase NM_0212880.03−0.558.0220.2750.235 7.787 0.006 0.785 8.572
Nitrogen Metabolism
ASNS asparagine synthetase NM_0120550.0120.54312.5030.022−0.475 12.978 0.001 −1.01811.96
CA13 carbonic anhydrase XIII NM_0244950.5080.1783.4180.017−0.632 7.984 0.014 −0.661 7.323
CA3
carbonic anhydrase III,
muscle specific NM_0076060.0080.17415.645 0.208 −0.833 12.791 0.003 −2.866 9.925
CA4 carbonic anhydrase IV NM_0076070.0310.7079.4660.0160.832 8.634 0.547 0.17 8.01
CA5B
carbonic anhydrase VB,
mitochondrial NM_0195130.015 0.97411.934 0.189 −0.239 11.687 0.006 −1.222 10.96
CA8 carbonic anhydrase VIII NM_0075920.2070.3395.4730.24−0.312 5.786 0.034 −0.6515.135
CA9 carbonic anhydrase IX NM_1393050.104−1.2513.2290.4620.517 2.712 0.035 1.768 4.48

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 63
Continued
CTH
cystathionase
(cystathionine
gamma-lyase)
NM_145953 0.02−0.6999.1250.2680.276 8.849 0.005 0.975 9.824
PDPR
pyruvate dehydrogenase
phosphatase
regulatory subunit
BB667201 0.0020.44210.1520.006−0.341 10.493 0 −0.783 9.71
PTPRG
protein tyrosine
phosphatase,
receptor type, G
NM_008981 0.0010.4998.830.009−0.328 9.158 0 −0.8278.331
VNN1 vanin 1 NM_011704 0.0030.913 9.7470.0190.614 9.133 0.173 −0.3 8.834
VNN2 vanin 2 NM_011979 0.0051.42910.815 0.745 −0.118 10.932 0.004 −1.5479.386
Alanine and Aspartate Metabolism
ADSL adenylosuccinate lyase NM_009634 0.1980.2810.0820.214−0.269 10.351 0.029 −0.55 9.801
ADSSL1
adenylosuccinate synthase
like 1 NM_007421 0.023−0.956 9.522 0.016 1.041 8.481 0.001 1.996 10.477
ASNS asparagine synthetase NM_012055 0.0120.54312.5030.022−0.475 12.978 0.001 −1.01811.96
ASS1 argininosuccinate synthetase 1 NM_007494 0.002−1.8456.4650.6940.154 6.31 0.002 1.999 8.309
CRAT carnitine acetyltransferase NM_007760 0.0030.60711.470.3120.123 4.974 0.002 −0.617 10.863
DDO D-aspartate oxidase NM_027442 0.0430.6627.7980.144 −0.436 8.234 0.005 −1.099 7.136
GOT1
glutamic-oxaloacetic
transaminase 1, soluble
(aspartate aminotransferase 1)
NM_010324 0.798−0.0529.4890.0380.51 8.978 0.026 0.5639.541
GPT2
glutamic pyruvate
transaminase (alanine
aminotransferase) 2
NM_173866 0.020.91711.372 0.027 −0.589 11.014 0.001 −1.1959.819
PC pyruvate carboxylase NM_008797 0.0530.35514.5850.334−0.157 14.741 0.013 −0.51114.23
PDHA1
(includes EG:5160)
pyruvate dehydrogenase
(lipoamide) alpha 1 NM_008810 0.0120.25514.6660.003−0.349 15.014 0 −0.603 14.411
PDHB
pyruvate dehydrogenase
(lipoamide) beta NM_024221 0.3060.14914.0830.019−0.774 10.036 0.006 −0.54113.934
Inositol Phosphate Metabolism
ACVR2A activin A receptor, type IIA NM_007396 0.06−0.3955.9980.1090.322 5.676 0.005 0.717 6.393
AKT2
v-akt murine thymoma
viral oncogene homolog 2 NM_001110200.020.69211.060.489 0.164 10.896 0.016 −0.43913
ARAF
v-raf murine sarcoma 3611
viral oncogene homolog NM_009703 0.0380.37610.450.2580.245 11.406 0.02
−0.912 3.647
CDC2
cell division cycle 2, G1 to S
and G2 to M NM_007659 0.013−1.3958.3420.021.253 7.088 0 2.6489.736
CDK6 cyclin-dependent kinase 6 NM_009873 0.024−0.7629.0290.0930.629 7.834 0.003 1.211 9.791
CDK7 cyclin-dependent kinase 7 NM_009874 0.043−0.5915.7520.161 −0.283 6.617 0.023 −0.5336.084
CSNK1D casein kinase 1, delta NM_027874 0.0360.59310.450.253−0.043 2.526 0.026 −0.3459.897
EIF2AK2
eukaryotic translation
initiation factor 2-alpha
kinase 2
NM_011163 0.0340.586.3760.2610.163 6.524 0.088 −0.4335.796
GRK5
G protein-coupled receptor
kinase 5 NM_018869 0.166−0.24210.3660.0280.436 9.93 0.004 0.67810.608
INPP1
inositol
polyphosphate-1-phosphatase NM_008384 0.0120.7988.6960.9870.004 8.692 0.013 −0.7947.898
INPP5D
inositol
polyphosphate-5-phosphatase,
145 kDa
NM_0011101920.028−0.5397.4770.0830.388 6.693 0.006 0.776 8.016
INPP5E
Inositol
polyphosphate-5-phosphatase,
72 kDa
NM_033134 0.0360.3738.1940.202−0.2 8.394 0.006 −0.5737.821
IRAK1
interleukin-1
receptor-associated
kinase 1
NM_008363 0.0080.41711.9850.062−0.131 8.168 0.003 −0.53 11.568

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 64
Continued
MAPK9
mitogen-activated
protein kinase 9 NM_016961 0.060.2157.4490.012−0.33 7.779 0.001 −0.545 7.234
NEK2
NIMA (never in
mitosis gene
a)-related kinase 2
BB203873 0.2530.0122.1350.0511.088 3.839 0.024 1.33 5.169
PAK1
p21/Cdc42/Rac1-activated
kinase 1 (STE20 homolog,
yeast)
NM_011035 0.036−0.9627.9840.3010.477 7.838 0.013 1.4469.283
PCTK3 PCTAIRE protein kinase 3 NM_008795 0.052−1.7666.542 0.001 3.965 2.577 0 5.73 8.308
PI4K2A
phosphatidylinositol
4-kinase type 2 alpha NM_145501 0.013−0.27711.3460.0020.453 7.825 0 0.61911.623
PI4K2B
phosphatidylinositol
4-kinase type 2 beta NM_025951 0.056−0.3558.6470.0180.693 6.639 0.002 0.7499.001
PIK3CA
phosphoinositide-3-kinase,
catalytic, alpha polypeptide NM_008839 0.0010.6456.7550.127−0.249 7.833 0 −0.815 6.11
PIK3CD
phosphoinositide-3-kinase,
catalytic, delta polypeptide NM_0010298370.053 −0.5486.2160.256−0.386 9.26 0.012
0.813 6.764
PIK3R1
phosphoinositide-3-kinase,
regulatory subunit 1 (alpha) NM_0010249550.0090.6289.6450.001 −0.697 13.043 0 −1.402 9.017
PIK3R3
phosphoinositide-3-kinase,
regulatory subunit 3 (gamma) NM_181585 0.281−0.2867.8270.060.555 7.271 0.012
0.841 8.112
PIM1 pim-1 oncogene NM_008842 0.032−1.33.5450.4590.18 8.558 0.06 1.086 4.845
PIP5K1C
phosphatidylinositol-4-
phosphate 5-kinase,
type I, gamma
NM_008844 0.057−0.4839.7210.6470.1 9.621 0.029 0.58210.204
PLCB4 phospholipase C, beta 4 NM_013829 0.0151.0364.2860.28−0.212 10.733 0.01 −1.1543.251
PLCD1 phospholipase C, delta 1 NM_019676 0.0130.64510.6520.094−0.374 11.027 0.001 −1.019 10.007
PLCD3 phospholipase C, delta 3 NM_152813 0.0560.6096.560.478−0.196 6.756 0.02 −0.806 5.951
PLCG2
phospholipase C,
gamma 2
(phosphatidylinositol-specific)
NM_172285 0.014−0.4759.2960.4390.116 9.181 0.005 0.5919.771
PLCL2 phospholipase C-like 2 NM_013880 0.031−0.3989.4470.3010.161 9.285 0.007 0.559 9.844
PRKAA1
protein kinase,
AMP-activated, alpha 1
catalytic subunit
NM_0010133670.0090.4086.520.001 −0.631 7.151 0 −1.0396.112
PRKCD protein kinase C, delta NM_011103 0.15−0.27311.2390.0330.451 10.788 0.004 0.72411.512
PRKCH protein kinase C, eta NM_008856 0.087−0.74310.472 0.0270.997 7.892 0.003 1.594 9.486
PRPF4B
PRP4 pre-mRNA processing
factor 4 homolog B (yeast) NM_013830 0.0080.3458.0060.071−0.264 9.994 0.002 −0.563 8.844
Glycosaminoglycan Degradation
AFP alpha-fetoprotein NM_007423 0.068−1.7082.7180.1140.381 3.333 0.022 0.6313.964
CHI3L3 chitinase 3-like 3 NM_009892 0.047−0.9976.054 0.0780.85 5.203 0.003 1.847 7.05
GALNS
galactosamine (N-acetyl)-
6-sulfate sulfatase
(Morquio syndrome,
mucopolysaccharidosis
type IVA)
NM_016722 0.129−0.2799.4910.080.334 9.157 0.008 0.6139.77
GLB1 galactosidase, beta 1 AW553762 0.0440.9177.970.0040.282 10.92 0.001 0.36911.288
GLB1L galactosidase, beta 1-like BB207162 0.0050.6368.0140.207−0.019 2.343 0.006 −0.6157.378
GLB1L2 galactosidase, beta 1-like 2 NM_153803 0.0280.50814.0960.033−0.47 13.134 0.002 −0.879 12.256
GUSB glucuronidase, beta NM_010368 0.101−0.43212.270.0230.747 10.177 0.002 1.093 12.702
IDS
iduronate 2-sulfatase
(Hunter syndrome) NM_0010389900.0250.3037.6050.028 −0.268 12.593 0.001 −0.527 12.066
MGEA5
meningioma expressed
antigen 5 (hyaluronidase) NM_023799 0.0040.3810.5460.074−0.234 12.444 0.001 −0.535 10.166
SULF1 sulfatase 1 NM_172294 0.0740.66111.0970.284−0.315 2.943 0.049 −0.753 10.436
SULF2 sulfatase 2 NM_028072 0.0020.6612.8890.5450.245 8.922 0.003 −0.627 12.229

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 65
Supplement Table 4.
FUP/FV FUP/FC FV/FC
Name Description RefSeq ID
p-value Log
Ratio Intensity p-valueLog Ratio Intensity p-value Log Ratio Intensity
Cell Cycle: G2/M DNA Damage
Checkpoint Regulation
BRCA1 breast cancer 1, early onset NM_009764 0.045−1.7214.598 0.2650.8433.755 0.009 2.5646.318
CCNB1 cyclin B1 NM_172301 0.026−1.5715.055 0.0641.2143.841 0.002 2.7856.626
CCNB2 cyclin B2 NM_007630 0.016−1.527.083 0.0311.2825.8 0.001 2.8028.602
CDC2
cell division cycle 2,
G1 to S and G2 to M NM_007659 0.013−1.3958.342 0.021.2537.088 0 2.6489.736
CDKN1A
cyclin-dependent kinase
inhibitor 1A (p21, Cip1) NM_0011110990.026 −0.6799.893 0.0011.4688.425 0 2.146 10.571
SKP2
S-phase kinase-associated
protein 2 (p45) NM_013787 0.214−0.5993.876 0.1380.7373.139 0.02
1.3374.476
TOP2A
topoisomerase (DNA) II
alpha 170 kDa NM_011623 0.023−1.536.184 0.0761.0835.1 0.002 2.6147.714
UBD ubiquitin D NM_023137 0.022−2.072 12.1590.0014.4757.683 0 6.54714.23
YWHAE
tyrosine 3-monooxygenase/
tryptophan 5-monooxygenase
activation protein, epsilon
polypeptide
BF714941 0.0121.2195.874 0.053−0.2678.76 0.003 −1.5984.655
YWHAZ
tyrosine 3-monooxygenase/
tryptophan 5-monooxygenase
activation protein, zeta
polypeptide
NM_011740 0.008−0.8767.273 0.447−0.1887.461 0.024 0.6888.148
Glucocorticoid Receptor Signaling
AGT
angiotensinogen (serpin
peptidase inhibitor, clade
A, member 8)
NM_007428 0.0121.90312.8130.207 −0.77213.584 0.002 −2.67410.91
AR
androgen receptor
(dihydrotestosterone receptor;
testicular feminization; spinal
and bulbar muscular atrophy;
Kennedy disease)
NM_013476 0.0010.86610.48 0.031−0.44510.925 0 −1.3119.615
BCL3 B-cell CLL/lymphoma 3 NM_033601 0.03−0.3928.281 0.0020.6847.596 0 1.0768.672
CCL13
chemokine (C-C motif)
ligand 13 NM_011333 0.001−1.42510.7870 1.6839.103 0 3.109 12.212
CCL3
chemokine (C-C motif)
ligand 3 NM_011337 0.033−1.3164.068 0.0191.5052.563 0.001 2.8215.383
CD163 CD163 molecule NM_053094 0.0720.68110.3430.108−0.59110.934 0.006 −1.2729.662
CDKN1A
cyclin-dependent kinase
inhibitor 1A (p21, Cip1) NM_0011110990.026 −0.6799.893 0.0011.4688.425 0 2.146 10.571
CDKN1C
cyclin-dependent kinase
inhibitor 1C (p57, Kip2) NM_009876 0.2230.2239.726 0.008−0.63410.36 0.002
−0.8579.503
CXCL3
chemokine (C-X-C motif)
ligand 3 NM_009140 0.9190.0614.962 0.0481.4223.541 0.055 1.3614.901
ESR1 estrogen receptor 1 NM_007956 0.0410.52 6.097 0.033−0.5516.648 0.002 −1.0715.577

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 66
Continued
FCGR1A
Fc fragment of IgG, high
affinity Ia, receptor (CD64) NM_010186 0.048−1.1676.7360.2240.6139.285 0.015 1.513 10.798
FKBP5 FK506 binding protein 5 NM_010220 0.0490.842 7.948 0.226−0.249 11.349 0.054 −0.439 10.909
FOS v-fos FBJ murine osteosarcoma
viral oncogene homolog NM_010234 0.077−1.08910.7590.2070.72510.034 0.012 1.813 11.848
IKBKE
inhibitor of kappa light
polypeptide gene enhancer
in B-cells, kinase epsilon
NM_019777 0.013−0.5558.5310.0290.4568.075 0.001 1.012 9.086
IL1R2 interleukin 1 receptor, type II NM_010555 0.002−1.4532.7190.3180.3052.413 0.001 1.759 4.172
IL1RN interleukin 1 receptor antagonist NM_0010397010.005−1.8052.2030 3.3 3.963 0 4.59 8.553
MAP2K7 mitogen-activated protein
kinase kinase 7 NM_0010425570.1140.6134.4990.2710.3483.444 0.032 −0.912 3.887
MAPK14 mitogen-activated protein
kinase 14 NM_011951 0.0020.8467.58 0.062−0.06412.45 0 −0.194 12.256
NCOR1 nuclear receptor co-repressor 1 NM_011308 0.0020.864 8.333 0.039−0.595 5.03 0.001 −1.134 7.47
NR3C1
nuclear receptor subfamily 3,
group C, member 1
(glucocorticoid receptor)
NM_008173
0 0 0.988 8.9460.001−0.54212.348 0 −1.444 7.958
NRIP1 nuclear receptor
interacting protein 1 NM_173440 0.0020.67510.3560.004−0.57210.928 0 −1.247 9.681
PCK1 phosphoenolpyruvate
carboxykinase 1 (soluble) NM_011044 0.0022.19312.8270.7830.18112.921 0.002 −2.229 10.633
PIK3CA phosphoinositide-3-kinase,
catalytic, alpha polypeptide NM_008839 0.0010.6456.7550.127−0.2497.833 0 −0.815 6.11
PIK3CD phosphoinositide-3-kinase,
catalytic, delta polypeptide NM_0010298370.053 −0.548 6.2160.256−0.386 9.26 0.012 0.813 6.764
PIK3R1 phosphoinositide-3-kinase,
regulatory subunit 1 (alpha) NM_001024955 0.0090.6289.6450.001−0.69713.043 0 −1.402 9.017
PIK3R3 phosphoinositide-3-kinase,
regulatory subunit 3 (gamma) NM_181585 0.281−0.2867.8270.060.5557.271 0.012 0.841 8.112
PIK3R5 phosphoinositide-3-kinase,
regulatory subunit 5 NM_177320 0.155−0.692 7.330.0221.2996.031 0.003 1.991 8.022
SERPINE1
serpin peptidase inhibitor,
clade E (nexin,
plasminogen activator
inhibitor type 1), member 1
NM_008871 0.044−1.6158.7570.4030.5788.179 0.013 2.194 10.373
SMARCA2
SWI/SNF related, matrix
associated, actin dependent
regulator of chromatin,
subfamily a, member 2
NM_011416 0 0.5199.8730.001−0.32510.198 0 −0.844 9.354
TAF15
TAF15 RNA polymerase
II, TATA box binding
protein (TBP)-associated
factor, 68 kDa
NM_027427 0.0061.104 4.1510.173−0.647 3.913 0.031 −0.753 3.047
TAF6L
TAF6-like RNA polymerase
II, p300/CBP-associated
factor (PCAF)-associated
factor, 65 kDa
NM_146092 0.061−0.4017.9430.0570.4117.532 0.003 0.812 8.343
TAF9B
TAF9B RNA polymerase
II, TATA box binding
protein (TBP)-associated
factor, 31 kDa
NM_001001176 0.0060.868 8.5820.081−0.4489.03 0.001 −1.316 7.713
TGFB3 transforming growth factor,
beta 3 NM_009368 0.0010.49510.6690.009−0.33711.006 0 −0.832 10.174

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 67
Continued
TGFBR2 transforming growth factor,
beta receptor II (70/80 kDa) NM_009371 0.0010.966 9.9720.2180.228 9.744 0.004 −0.739 9.005
TRA@ T cell receptor alpha locus XM_001471582 0.038−1.4388.857 0.0351.472 7.385 0.002 2.909 10.295
VCAM1 vascular cell adhesion
molecule 1 NM_011693 0.078−0.7066.1650.2250.452 5.714 0.013
1.158 6.872
PPARa/RXRa Activation
ACVR1C activin A receptor,
type IC NM_001033369 0.0010.8598.0510.002 −0.725 8.777 0 −1.584 7.192
ADCY7 adenylate cyclase 7 NM_001037723 0.08−0.75810.6450.2040.467 7.078 0.019 1.034 8.113
BCL3 B-cell CLL/lymphoma 3 NM_033601 0.03−0.3928.2810.0020.684 7.596 0 1.076 8.672
CYP2C44
cytochrome P450, family
2, subfamily c,
polypeptide 44
NM_001001446 0.001−2.8145.549 0.0022.405 3.144 0 5.219 8.363
CYP2C70
cytochrome P450, family
2, subfamily c,
polypeptide 70
NM_145499 0.038−1.2892.7230.4260.418 2.305 0.012 1.707 4.012
GK glycerol kinase NM_008194 0.03−0.8977.8210.5640.193 6.204 0.018 1.006 7.21
GPD2
glycerol-3-phosphate
dehydrogenase 2
(mitochondrial)
NM_010274 0.0081.0845.6570.001 −1.621 7.277 0 −2.704 4.573
IKBKE
inhibitor of kappa
light polypeptide gene
enhancer in B-cells,
kinase epsilon
NM_019777 0.013−0.5558.5310.0290.456 8.075 0.001 1.012 9.086
IL1R2 interleukin 1 receptor,
type II NM_010555 0.002−1.4532.7190.3180.305 2.413 0.001 1.759 4.172
INSR insulin receptor NM_001033381 0 0.6689.9370.022−0.275 10.212 0 −0.943 9.269
IRS1 insulin receptor
substrate 1 NM_010570 0.0061.38711.2580.089 −0.681 11.939 0.001 −2.067 9.872
MAP2K7 mitogen-activated
protein kinase kinase 7 NM_001042557 0.1140.613 4.4990.2710.348 3.444 0.032
−0.912 3.887
MAPK14 mitogen-activated
protein kinase 14 NM_011951 0.0020.8467.580.062 −0.064 12.45 0 −0.19412.256
NCOR1 nuclear receptor
co-repressor 1 NM_011308 0.0020.8648.3330.039 −0.595 5.03 0.001 −1.134 7.47
PLCB4 phospholipase C,
beta 4 NM_013829 0.0151.0364.2860.28−0.212 10.733 0.01 −1.154 3.251
PLCD1 phospholipase C,
delta 1 NM_019676 0.0130.64510.6520.094−0.374 11.027 0.001 −1.019 10.007
PLCD3 phospholipase C,
delta 3 NM_152813 0.0560.6096.560.478−0.196 6.756 0.02 −0.806 5.951
SLC27A1
solute carrier family
27 (fatty acid transporter),
member 1
NM_011977 0.0040.81311.7680.0160.619 11.149 0.342 −0.19410.955
TGFB3 transforming growth
factor, beta 3 NM_009368 0.0010.49510.6690.009−0.337 11.006 0 −0.832 10.174
TGFBR2
transforming growth
factor, beta receptor
II (70/80 kDa)
NM_009371 0.0010.9669.9720.2180.228 9.744 0.004 −0.739 9.005
Acute Phase Response Signaling

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 68
Continued
AGT
angiotensinogen
(serpin peptidase
inhibitor, clade
A, member 8)
NM_007428 0.0121.90312.813 0.207 −0.772 13.584 0.002 −2.674 10.91
BCL3 B-cell
CLL/lymphoma 3 NM_033601 0.03−0.3928.2810.0020.684 7.596 0 1.076 8.672
C2 complement
component 2 NM_013484 0.0050.85912.656 0.057 −0.441 14.039 0.001 −1.319 11.797
CP ceruloplasmin
(ferroxidase) NM_0010426110.003 0.86711.589 0.016 −0.513 11.028 0 −1.27810.722
FOS
v-fos FBJ murine
osteosarcoma viral
oncogene homolog
NM_010234 0.077−1.08910.7590.2070.725 10.034 0.012 1.813 11.848
FRAP1
FK506 binding
protein 12-rapamycin
associated protein 1
NM_020009 0.05−0.8254.1570.274 −0.144 10.371 0.031 0.9384.981
HMOX1 heme oxygenase
(decycling) 1 NM_010442 0.242−0.4959.7170.1940.557 9.16 0.032
1.052 10.212
IKBKE
inhibitor of kappa
light polypeptide
gene enhancer in
B-cells, kinase epsilon
NM_019777 0.013−0.5558.5310.0290.456 8.075 0.001 1.012 9.086
IL1RN interleukin 1 receptor
antagonist NM_0010397010.005 −1.8052.2030 3.3 3.963 0 4.59 8.553
MAP2K7 mitogen-activated
protein kinase kinase 7 NM_0010425570.1140.613 4.4990.2710.348 3.444 0.032
−0.912 3.887
MAPK14 mitogen-activated
protein kinase 14 NM_011951 0.0020.8467.580.062 −0.064 12.45 0 −0.19412.256
NR3C1
nuclear receptor
subfamily 3, group
C, member 1
(glucocorticoid receptor)
NM_008173 0 0.9888.9460.001−0.542 12.348 0 −1.444 7.958
ORM1 orosomucoid 1 NM_011016 0.001−1.356.2370 1.542 4.695 0 2.8927.587
PIK3CA phosphoinositide-3-kinase,
catalytic, alpha polypeptide NM_008839 0.0010.6456.7550.127−0.249 7.833 0 −0.8156.11
PIK3CD phosphoinositide-3-kinase,
catalytic, delta polypeptide NM_0010298370.053 −0.5486.2160.256−0.386 9.26 0.012
0.813 6.764
PIK3R1 phosphoinositide-3-kinase,
regulatory subunit 1 (alpha) NM_0010249550.0090.6289.6450.001−0.697 13.043 0 −1.402 9.017
PIK3R3 phosphoinositide-3-kinase,
regulatory subunit 3 (gamma) NM_181585 0.281−0.2867.8270.060.555 7.271 0.012
0.841 8.112
RBP7 retinol binding protein 7,
cellular NM_022020 0.2090.54710.1210.0081.48 8.64 0.052 0.9349.574
SAA2 serum amyloid A2 NM_011315 0.015−2.32311.2670.7380.245 11.022 0.01 2.56813.59
SERPINA1
serpin peptidase inhibitor,
clade A (alpha-1
antiproteinase, antitrypsin),
member 1
NM_009243 0.002−1.0464.6530.2640.242 4.411 0 1.288 5.699
SERPINE1
serpin peptidase inhibitor,
clade E (nexin, plasminogen
activator inhibitor type 1),
member 1
NM_008871 0.044−1.6158.7570.4030.578 8.179 0.013 2.194 10.373
SERPINF1
serpin peptidase inhibitor,
clade F (alpha-2 antiplasmin,
pigment epithelium
derived factor), member 1
NM_011340 0.570.09213.7650.0010.924 12.841 0.001 0.75713.916

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 69
Continued
TNFRSF11B
tumor necrosis factor
receptor superfamily,
member 11b
(osteoprotegerin)
NM_008764 0.1470.5256.2 0.075−0.675 6.875 0.008 −1.2 5.675
P53 Signaling
BAX BCL2-associated X
protein NM_007527 0.033−0.45111.4660.0560.386 11.079 0.002 0.83711.917
BIRC5
baculoviral IAP
repeat-containing 5
(survivin)
NM_0010122730.03 −1.6556.710.0741.274 5.436 0.002 2.929 8.366
BRCA1 breast cancer 1,
early onset NM_009764 0.045−1.7214.5980.265 0.843 3.755 0.009 2.564 6.318
CDKN1A
cyclin-dependent
kinase inhibitor 1A
(p21, Cip1)
NM_0011110990.026−0.6799.8930.001 1.468 8.425 0 2.146 10.571
E2F1 E2F transcription factor 1 NM_007891 0.085−0.3546.9770.0160.663 8.141 0.002 0.904 7.331
GADD45B
growth arrest
and DNA-damage-inducible,
beta
NM_008655 0.003−0.94910.170.0890.407 9.762 0 1.356 11.118
HDAC9 histone deacetylase 9 NM_024124 0.11−0.4618.3630.1310.43 7.933 0.011 0.891 8.824
MAPK14 mitogen-activated protein
kinase 14 NM_011951 0.0020.8467.580.062 −0.064 12.45 0 −0.194 12.256
PIK3CA phosphoinositide-3-kinase,
catalytic, alpha polypeptide NM_008839 0.0010.6456.7550.127−0.249 7.833 0 −0.815 6.11
PIK3CD phosphoinositide-3-kinase,
catalytic, delta polypeptide NM_0010298370.053−0.5486.2160.256−0.386 9.26 0.012
0.813 6.764
PIK3R1 phosphoinositide-3-kinase,
regulatory subunit 1 (alpha) NM_0010249550.0090.6289.6450.001 −0.697 13.043 0 −1.402 9.017
PIK3R3 phosphoinositide-3-kinase,
regulatory subunit 3 (gamma) NM_181585 0.281−0.2867.8270.060.555 7.271 0.012
0.841 8.112
PIK3R5 phosphoinositide-3-kinase,
regulatory subunit 5 NM_177320 0.155−0.6927.330.0221.299 6.031 0.003 1.991 8.022
PLAGL1 pleiomorphic adenoma
gene-like 1 NM_009538 0.0021.07913.0070.029 −0.604 13.61 0 −1.68311.928
RB1 retinoblastoma 1
(including osteosarcoma) NM_009029 0.038−0.654.4830.0980.483 4.001 0.003
1.133 5.134
SIRT1
sirtuin (silent mating
type information regulation
2 homolog) 1 (S. cerevisiae)
NM_019812 0.1030.3527.590.048−0.451 8.041 0.004 −0.804 7.237
THBS1 thrombospondin 1 NM_011580 0.0011.0811.080.1990.399 11.387 0.002 −0.98410
WT1 Wilms tumor 1 NM_144783 0.0470.6898.5170.041−0.721 9.238 0.002 −1.411 7.827
IL-4 Signaling
FRAP1
FK506 binding protein
12-rapamycin associated
protein 1
NM_020009 0.05−0.8254.1570.274−0.144 10.371 0.031 0.938 4.981
HLA-DMB major histocompatibility
complex, class II, DM beta NM_010387 0.004−1.0389.3380.030.435 11.761 0 1.094 12.855
HMGA1 high mobility group
AT-hook 1 NM_0010254270.028−0.86710.8640.0230.911 9.953 0.001 1.778 11.731
IRS1 insulin receptor substrate 1 NM_010570 0.0061.38711.2580.089 −0.681 11.939 0.001 −2.067 9.872

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 70
Continued
NR3C1
nuclear receptor subfamily
3, group C, member 1
(glucocorticoid receptor)
NM_008173 0 0.9888.9460.001−0.542 12.348 0 −1.444 7.958
PIK3CA phosphoinositide-3-kinase,
catalytic, alpha polypeptide NM_008839 0.0010.6456.7550.127−0.249 7.833 0 −0.815 6.11
PIK3CD phosphoinositide-3-kinase,
catalytic, delta polypeptide NM_0010298370.053 −0.5486.2160.256−0.386 9.26 0.012
0.813 6.764
PIK3R1 phosphoinositide-3-kinase,
regulatory subunit 1 (alpha) NM_0010249550.0090.6289.6450.001 −0.697 13.043 0 −1.402 9.017
PIK3R3 phosphoinositide-3-kinase,
regulatory subunit 3 (gamma) NM_181585 0.281−0.2867.8270.060.555 7.271 0.012
0.841 8.112
PIK3R5 phosphoinositide-3-kinase,
regulatory subunit 5 NM_177320 0.155−0.6927.330.0221.299 6.031 0.003 1.9918.022
PI3K/AKT Signaling
BCL3 B-cell CLL/lymphoma 3 NM_033601 0.03−0.3928.2810.0020.684 7.596 0 1.0768.672
CDKN1A cyclin-dependent kinase
inhibitor 1A (p21, Cip1) NM_0011110990.026−0.679 9.893 0.001 1.468 8.425 0 2.146 10.571
CDKN1B cyclin-dependent kinase
inhibitor 1B (p27, Kip1) NM_009875 0.1250.398.6960.093−0.436 9.132 0.009
−0.826 8.306
EIF4EBP1
eukaryotic translation
initiation factor 4E
binding protein 1
NM_007918 0.0161.108 9.7080.8380.03 14.414 0.013 −1.158 8.599
FOXO1 forkhead box O1 NM_019739 0.0070.656 10.7560.1−0.323 11.079 0.001 −0.979 10.1
FRAP1
FK506 binding protein
12-rapamycin
associated protein 1
NM_020009 0.05−0.8254.1570.274−0.144 10.371 0.031 0.938 4.981
GYS1 glycogen synthase 1
(muscle) NM_030678 0.0111.0967.2940.493−0.225 7.52 0.005 −1.321 6.199
GYS2 glycogen synthase 2
(liver) NM_145572 0.005−1.678.426 0.085 0.809 7.617 0.001 2.479 10.096
IKBKE
inhibitor of kappa light
polypeptide gene enhancer
in B-cells, kinase epsilon
NM_019777 0.013−0.5558.5310.0290.456 8.075 0.001 1.012 9.086
MAPK8IP1 mitogen-activated protein
kinase 8 interacting protein 1 NM_011162 0.0071.177.2420.05−0.722 7.964 0.001 −1.892 6.071
PIK3CA phosphoinositide-3-kinase,
catalytic, alpha polypeptide NM_008839 0.0010.6456.7550.127−0.249 7.833 0 −0.815 6.11
PIK3CD phosphoinositide-3-kinase,
catalytic, delta polypeptide NM_0010298370.053 −0.5486.2160.256−0.386 9.26 0.012
0.813 6.764
PIK3R1 phosphoinositide-3-kinase,
regulatory subunit 1 (alpha) NM_0010249550.0090.6289.6450.001 −0.697 13.043 0 −1.402 9.017
PIK3R3
phosphoinositide-3-kinase,
regulatory subunit 3
(gamma)
NM_181585 0.281−0.2867.8270.060.555 7.271 0.012
0.841 8.112
PPP2R3A
(includes EG:5523)
protein phosphatase 2
(formerly 2A), regulatory
subunit B”, alpha
XM_0014743960.0070.4866.878 0.004 −0.55 7.428 0 −1.036 6.392
YWHAE
tyrosine 3-monooxygenase/
tryptophan 5-monooxygenase
activation protein, epsilon
polypeptide
BF714941 0.0121.2195.8740.053−0.267 8.76 0.003 −1.598 4.655
YWHAZ
tyrosine 3-monooxygenase/
tryptophan 5-monooxygenase
activation protein,
zeta polypeptide
NM_011740 0.008−0.8767.2730.447−0.188 7.461 0.024 0.6888.148

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 71
Continued
SAPK/JNK Signaling
GNG2 guanine nucleotide binding
protein (G protein), gamma 2 NM_0010386370.008 −1.1468.6580.1350.514 8.144 0.001 1.6619.804
GNG7 guanine nucleotide binding
protein (G protein), gamma 7 NM_0010386550.016 0.9666.2780.645 −0.142 6.42 0.008 −1.109 5.311
IRS1 insulin receptor substrate 1 NM_010570 0.0061.38711.258 0.089 −0.681 11.939 0.001 −2.067 9.872
MAP2K7 mitogen-activated protein
kinase kinase 7 NM_0010425570.1140.613 4.4990.2710.348 3.444 0.032
−0.912 3.887
MAP3K13 mitogen-activated protein
kinase kinase kinase 13 XM_0014808120.10.6764.220.4430 2.122 0.05
−0.853.543
MAP3K3 mitogen-activated protein
kinase kinase kinase 3 NM_011947 0.049−2.0115.5490.137 −1.412 6.962 0.092 −0.237 9.719
MAP4K1 mitogen-activated protein
kinase kinase kinase kinase 1 NM_008279 0.2−0.2527.7330.002 0.867 6.866 0.001 1.119 7.985
MAPK8IP1 mitogen-activated protein
kinase 8 interacting protein 1 NM_011162 0.0071.177.2420.05 −0.722 7.964 0.001 −1.892 6.071
PIK3CA phosphoinositide-3-kinase,
catalytic, alpha polypeptide NM_008839 0.0010.6456.7550.127−0.249 7.833 0 −0.815 6.11
PIK3CD phosphoinositide-3-kinase,
catalytic, delta polypeptide NM_0010298370.053 −0.5486.2160.256 −0.386 9.26 0.012
0.813 6.764
PIK3R1 phosphoinositide-3-kinase,
regulatory subunit 1 (alpha) NM_0010249550.0090.6289.6450.001−0.697 13.043 0 −1.402 9.017
PIK3R3 phosphoinositide-3-kinase,
regulatory subunit 3 (gamma) NM_181585 0.281−0.2867.8270.060.555 7.271 0.012
0.841 8.112
PIK3R5 phosphoinositide-3-kinase,
regulatory subunit 5 NM_177320 0.155−0.6927.330.022 1.299 6.031 0.003 1.9918.022
TRA@ T cell receptor alpha locus XM_0014715820.038−1.4388.8570.035 1.472 7.385 0.002 2.909 10.295
TRG@ T cell receptor gamma locus NM_011558 0.2620.3963.9950.072−0.695 4.69 0.013 −1.093.599
Leukocyte Extravasation Signaling
ACTN1 actinin, alpha 1 NM_134156 0.032−0.7865.7060.040.743 8.142 0.002 1.523 6.492
ACTN3 actinin, alpha 3 NM_013456 0.2210.6127.4250.03−1.26 8.685 0.005 −1.873 6.813
ARHGAP4 Rho GTPase activating
protein 4 NM_138630 0.022−0.6125.9380.2620.249 5.689 0.005
0.861 6.55
ARHGAP6 Rho GTPase activating
protein 6 NM_009707 0.08−0.9825.4210.6880.199 5.222 0.044 1.1816.404
ARHGAP9 Rho GTPase activating
protein 9 NM_146011 0.027−0.8869 0.0320.848 8.152 0.001 1.735 9.887
BTK Bruton agammaglobulinemia
tyrosine kinase NM_013482 0.009−1.0579.3760.6070.153 9.223 0.005 1.21 10.433
CD44 CD44 molecule
(Indian blood group) NM_0010391500.036−0.90610.775 0.0191.077 6.791 0.001 1.916 8.707
CLDN12 claudin 12 NM_022890 0.0350.5237.8490.039−0.504 8.353 0.002 −1.027 7.326
CLDN5
claudin 5 (transmembrane
protein deleted in
velocardiofacial syndrome)
NM_013805 0.0291.09612.816 0.0450.977 11.839 0.771 −0.119 11.72
CTNNA1
catenin
(cadherin-associated
protein), alpha 1, 102 kDa
NM_009818 0.030.6665.0070.129−0.096 13.283 0.005 −1.025 4.342

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 72
Continued
CXCR4 chemokine (C-X-C motif)
receptor 4 NM_009911 0.413−0.3977 0.1250.8 6.2 0.037 1.198 7.397
CYBA cytochrome b-245, alpha
polypeptide NM_007806 0.068−0.39913.6560.0250.532 13.123 0.002 0.932 14.055
CYBB
cytochrome b-245,
beta polypeptide
(chronic granulomatous
disease)
NM_007807 0.045−0.56910.7560.0870.461 10.295 0.004 1.03 11.325
DLC1 deleted in liver cancer 1 NM_015802 0.0510.40312.010.007−0.554 9.799 0.001 −0.823 8.976
ITGB2
integrin, beta 2 (complement
component 3 receptor 3 and 4
subunit)
NM_008404 0.077−0.45613.3080.0110.774 12.534 0.001 1.229 13.764
MAPK14 mitogen-activated protein
kinase 14 NM_011951 0.0020.8467.580.062 −0.064 12.45 0 −0.19412.256
MMP11 matrix metallopeptidase 11
(stromelysin 3) NM_008606 0.139−0.6367.5530.4180.326 7.227 0.041
0.962 8.189
MMP12 matrix metallopeptidase 12
(macrophage elastase) NM_008605 0.447−0.68713.129 0.0122.956 10.173 0.005 3.643 13.816
MMP13 matrix metallopeptidase 13
(collagenase 3) NM_008607 0.082−1.4772.740.5460.455 2.285 0.033 1.932 4.217
MMP3 matrix metallopeptidase 3
(stromelysin 1, progelatinase) NM_010809 0.207−1.3035.9230.193 1.348 4.574 0.027 2.651 7.226
MMP9
matrix metallopeptidase 9
(gelatinase B, 92 kDa
gelatinase, 92 kDa type
IV collagenase)
NM_013599 0.0812.2657.7870.268 −1.057 9.127 0.019 −3.4115.522
NCF1C neutrophil cytosolic
factor 1C pseudogene NM_010876 0.157−0.22211.784 0.0031.001 7.382 0.001 0.76612.007
NCF2
neutrophil cytosolic
factor 2 (65 kDa, chronic
granulomatous disease,
autosomal 2)
NM_010877 0.021−0.64410.2810.0590.483 9.798 0.001 1.126 10.924
NCF4 neutrophil cytosolic
factor 4, 40 kDa NM_008677 0.024−0.5969.7870.0280.575 9.212 0.001
1.171 10.383
PECAM1
platelet/endothelial
cell adhesion molecule
(CD31 antigen)
NM_001032378 0.0110.891 9.6430.1420.424 9.219 0.112 −0.4678.752
PIK3CA phosphoinositide-3-kinase,
catalytic, alpha polypeptide NM_008839 0.0010.6456.7550.127−0.249 7.833 0 −0.8156.11
PIK3CD phosphoinositide-3-kinase,
catalytic, delta polypeptide NM_001029837 0.053−0.5486.2160.256 −0.386 9.26 0.012
0.813 6.764
PIK3R1 phosphoinositide-3-kinase,
regulatory subunit 1 (alpha) NM_001024955 0.0090.628 9.6450.001−0.697 13.043 0 −1.402 9.017
PIK3R3 phosphoinositide-3-kinase,
regulatory subunit 3 (gamma) NM_181585 0.281−0.2867.8270.060.555 7.271 0.012
0.841 8.112
PIK3R5 phosphoinositide-3-kinase,
regulatory subunit 5 NM_177320 0.155−0.6927.330.022 1.299 6.031 0.003 1.991 8.022
PRKCH protein kinase C, eta NM_008856 0.087−0.74310.4720.0270.997 7.892 0.003 1.594 9.486
PRKD1 protein kinase D1 NM_008858 0 0.37710.7130 −0.515 11.227 0 −0.89210.336
RDX radixin NM_001104616 0 1.0157.9 0.003−0.276 12.632 0 −0.64511.988
SELPLG selectin P ligand NM_009151 0.01−0.60411.2240.1870.248 10.976 0.002 0.852 11.828
TEC tec protein tyrosine kinase NM_001113460 0.039−0.42210.1260.0050.697 9.429 0 1.119 10.548

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 73
Continued
TIMP1 TIMP metallopeptidase
inhibitor 1 NM_001044384 0.023−1.0259.675 0.0320.94 8.734 0.001 1.96510.699
TIMP3
TIMP metallopeptidase
inhibitor 3 (Sorsby
fundus dystrophy,
pseudoinflammatory)
NM_011595 0 1.0669.0760.393 −0.121 12.275 0 −1.0128.01
TIMP4 TIMP metallopeptidase
inhibitor 4 NM_080639 0.0180.77213.3670.404−0.217 13.585 0.006 −0.99 12.595
VAV1 vav 1 guanine nucleotide
exchange factor NM_011691 0.044−0.7045.7550.2090.391 5.363 0.007
1.095 6.458
VAV3 vav 3 guanine nucleotide
exchange factor NM_020505 0.072−0.7688.7430.1160.582 3.591 0.009
1.336 9.51
VCAM1 vascular cell adhesion
molecule 1 NM_011693 0.078−0.7066.1650.2250.452 5.714 0.013
1.158 6.872
WAS Wiskott-Aldrich syndrome
(eczema-thrombocytopenia) NM_009515 0.028−0.6238.9820.0660.485 8.497 0.002
1.107 9.604
Insulin Receptor Signaling
ACLY ATP citrate lyase NM_134037 0.3110.3812.3370.003−0.937 14.13 0.001 −1.14212.988
EIF4EBP1
eukaryotic translation
initiation factor 4E
binding protein 1
NM_007918 0.0161.108 9.7080.8380.03 14.414 0.013 −1.158 8.599
FOXO1 forkhead box O1 NM_019739 0.0070.656 10.7560.1−0.323 11.079 0.001 −0.97910.1
FRAP1
FK506 binding protein
12-rapamycin
associated protein 1
NM_020009 0.05−0.8254.1570.274 −0.144 10.371 0.031 0.9384.981
GYS1 glycogen synthase 1
(muscle) NM_030678 0.0111.0967.2940.493 −0.225 7.52 0.005 −1.321 6.199
GYS2 glycogen synthase 2
(liver) NM_145572 0.005−1.678.426 0.0850.809 7.617 0.001 2.47910.096
INSR insulin receptor NM_001033381 0 0.6689.9370.022−0.275 10.212 0 −0.943 9.269
IRS1 insulin receptor substrate 1 NM_010570 0.0061.38711.2580.089 −0.681 11.939 0.001 −2.0679.872
PIK3CA phosphoinositide-3-kinase,
catalytic, alpha polypeptide NM_008839 0.0010.6456.7550.127−0.249 7.833 0 −0.815 6.11
PIK3CD phosphoinositide-3-kinase,
catalytic, delta polypeptide NM_001029837 0.053−0.5486.2160.256 −0.386 9.26 0.012
0.813 6.764
PIK3R1 phosphoinositide-3-kinase,
regulatory subunit 1 (alpha) NM_001024955 0.0090.6289.6450.001−0.697 13.043 0 −1.4029.017
PIK3R3 phosphoinositide-3-kinase,
regulatory subunit 3 (gamma) NM_181585 0.281−0.2867.8270.060.555 7.271 0.012
0.841 8.112
PIK3R5 phosphoinositide-3-kinase,
regulatory subunit 5 NM_177320 0.155−0.6927.330.0221.299 6.031 0.003 1.991 8.022
PRKCH protein kinase C, eta NM_008856 0.087−0.74310.4720.0270.997 7.892 0.003 1.5949.486
SLC2A4
solute carrier family 2
(facilitated glucose
transporter), member 4
NM_009204 0.0291.36812.8890.309 −0.393 12.374 0.014 −1.20511.169
STXBP4 syntaxin binding protein 4 --- 0.0030.8585.130.567−0.11 5.239 0.002 −0.968 4.271
VAMP2 vesicle-associated membrane
protein 2 (synaptobrevin 2) NM_009497 0.0790.4647.8150.081−0.46 8.274 0.005
−0.924 7.351
Xenobiotic Metabolism Signaling

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 74
Continued
ABCB1
ATP-binding cassette,
sub-family B (MDR/TAP),
member 1
NM_011076 0.0060.7615.9880.157−0.401 8.141 0.001 −1.0525.227
ALDH3B1 aldehyde dehydrogenase 3
family, member B1 NM_026316 0.017−0.567.8480.0460.431 7.417 0.001 0.992 8.409
ALDH5A1
aldehyde dehydrogenase 5
family, member
A1 (succinate-semialdehyde
dehydrogenase)
NM_172532 0.0120.80210.108 0.459−0.18 10.288 0.004 −0.9829.306
ALDH6A1 aldehyde dehydrogenase 6
family, member A1 NM_134042 0.0020.50312.5660.009−0.359 12.925 0 −0.862 12.064
ARNT aryl hydrocarbon receptor
nuclear translocator NM_0010377370.01 0.8316.1190.002 −0.259 8.705 0 −0.4258.28
CAMK2D
calcium/
calmodulin-dependent
protein kinase (CaM kinase)
II delta
NM_0010254380.062 0.0872.365 0.496 −0.25 7.43 0.038 −0.902 6.528
CES1
(includes EG:1066)
carboxylesterase 1
(monocyte/macrophage
serine esterase 1)
NM_053200 0.0071.03613.6470.27−0.33 13.056 0.002 −1.382 11.674
CHST11
carbohydrate
(chondroitin 4)
sulfotransferase 11
NM_021439 0.112−0.2742.4180.0250.687 8.607 0.01 0.85 9.457
CITED2
Cbp/p300-interacting
transactivator, with
Glu/Asp-rich
carboxy-terminal domain, 2
NM_010828 0.0280.61511.6780.162−0.343 12.022 0.004 −0.958 11.064
CUL3 cullin 3 NM_016716 0.0010.5998.0510.017−0.329 8.38 0 −0.9287.452
FMO1 flavin containing
monooxygenase 1 NM_010231 0.0330.90913.4440.163 −0.526 13.971 0.004 −1.435 12.536
FMO5 flavin containing
monooxygenase 5 NM_010232 0
1.1696.8380.077 −0.228 7.066 0 −1.3965.669
GSTA3 glutathione
S-transferase A3 NM_0010773530.061 0.95311.4150.127 −0.725 9.233 0.006 −1.6567.577
GSTA4 glutathione
S-transferase A4 NM_010357 0.040.85311.386 0.122−0.589 11.975 0.004 −1.441 10.533
GSTT1 glutathione
S-transferase theta 1 NM_008185 0.0130.5912.7910.026−0.502 13.293 0.001 −1.092 12.201
HMOX1 heme oxygenase
(decycling) 1 NM_010442 0.242−0.4959.7170.1940.557 9.16 0.032
1.052 10.212
KEAP1
kelch-like
ECH-associated
protein 1
NM_0011103050.017 0.972 9.3520.1740.466 8.886 0.145 −0.5058.381
LIPA
lipase A, lysosomal
acid, cholesterol esterase
(Wolman disease)
NM_0011111000.044 −0.971 9.896 0.027 0.828 12.45 0.002 1.498 13.949
MAOB monoamine oxidase B NM_172778 0.0380.46312.20.035−0.473 12.673 0.002 −0.936 11.737
MAP2K7 mitogen-activated protein
kinase kinase 7 NM_0010425570.1140.613 4.4990.2710.348 3.444 0.032
−0.912 3.887
MAP3K3 mitogen-activated protein
kinase kinase kinase 3 NM_011947 0.049−2.0115.5490.137−1.412 6.962 0.092 −0.2379.719
MAPK14 mitogen-activated
protein kinase 14 NM_011951 0.0020.8467.580.062−0.064 12.45 0 −0.194 12.256
NFKB2
nuclear factor of kappa
light polypeptide gene
enhancer in B-cells
2 (p49/p100)
NM_019408 0.3−0.2838.3790.0450.625 7.754 0.01 0.908 8.662

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 75
Continued
NRIP1 nuclear receptor
interacting protein 1 NM_173440 0.0020.67510.3560.004−0.572 10.928 0 −1.247 9.681
PIK3CA phosphoinositide-3-kinase,
catalytic, alpha polypeptide NM_008839 0.0010.6456.7550.127−0.249 7.833 0 −0.815 6.11
PIK3CD phosphoinositide-3-kinase,
catalytic, delta polypeptide NM_0010298370.053 −0.5486.2160.256−0.386 9.26 0.012
0.813 6.764
PIK3R1 phosphoinositide-3-kinase,
regulatory subunit 1 (alpha) NM_0010249550.0090.6289.6450.001 −0.697 13.043 0 −1.402 9.017
PIK3R3 phosphoinositide-3-kinase,
regulatory subunit 3 (gamma) NM_181585 0.281−0.2867.8270.060.555 7.271 0.012
0.841 8.112
PIK3R5 phosphoinositide-3-kinase,
regulatory subunit 5 NM_177320 0.155−0.6927.330.0221.299 6.031 0.003 1.9918.022
PPP2R3A
(includes EG:5523)
protein phosphatase 2
(formerly 2A), regulatory
subunit B”, alpha
XM_0014743960.0070.4866.878 0.004 −0.55 7.428 0 −1.036 6.392
PRKCH protein kinase C,
eta NM_008856 0.087−0.743 10.4720.0270.997 7.892 0.003 1.5949.486
PRKD1 protein kinase D1 NM_008858 0 0.37710.7130 −0.515 11.227 0 −0.892 10.336
SULT1A1
sulfotransferase family,
cytosolic, 1A,
phenol-preferring,
member 1
NM_133670 0.0540.63513.7090.529−0.179 13.888 0.022 −0.814 13.073
SULT1E1
sulfotransferase family
1E, estrogen-preferring,
member 1
NM_023135 0.0560.44610.5030.004−0.856 11.36 0 −1.303 10.057
LPS/IL-1 Mediated Inhibition
of RXR Function
ABCB1
ATP-binding cassette,
sub-family
B (MDR/TAP),
member 1
NM_011076 0.0060.7615.9880.157−0.401 8.141 0.001 −1.052 5.227
ABCG1
ATP-binding cassette,
sub-family G (WHITE),
member 1
NM_009593 0.097−0.535 11.6240.0220.827 10.798 0.002 1.361 12.159
ALDH3B1 aldehyde dehydrogenase
3 family, member B1 NM_026316 0.017−0.567.8480.0460.431 7.417 0.001
0.992 8.409
ALDH5A1
aldehyde dehydrogenase
5 family, member
A1 (succinate-semialdehyde
dehydrogenase)
NM_172532 0.0120.80210.1080.459−0.18 10.288 0.004 −0.982 9.306
ALDH6A1 aldehyde dehydrogenase
6 family, member A1 NM_134042 0.0020.50312.5660.009−0.359 12.925 0 −0.862 12.064
APOC2 apolipoprotein C-II NM_009695 0.187−0.449.3160.0730.639 8.677 0.01 1.08 9.756
APOC4
(includes EG:346) apolipoprotein C-IV NM_007385 0 −2.2482.1260.9960.001 2.125 0 2.2494.375
CHST11
carbohydrate
(chondroitin 4)
sulfotransferase 11
NM_021439 0.112−0.2742.4180.0250.687 8.607 0.01 0.85 9.457
FABP4 fatty acid binding
protein 4, adipocyte NM_024406 0.0011.77110.720.438−0.247 10.967 0 −2.018 8.949
FABP5
fatty acid binding
protein 5
(psoriasis-associated)
NM_010634 0.018−0.47113.2310.0070.594 12.636 0 1.065 13.702
FABP7 fatty acid binding
protein 7, brain NM_021272 0.032−1.602 5.9560.017 1.882 4.074 0.001 3.4847.558
FMO1 flavin containing
monooxygenase 1 NM_010231 0.0330.90913.4440.163 −0.526 13.971 0.004 −1.435 12.536

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 76
Continued
FMO5 flavin containing
monooxygenase 5 NM_010232 0 1.1696.8380.077−0.228 7.066 0 −1.396 5.669
GSTA3 glutathione
S-transferase A3 NM_0010773530.061 0.95311.415 0.127 −0.725 9.233 0.006 −1.656 7.577
GSTA4 glutathione
S-transferase A4 NM_010357 0.040.85311.386 0.122 −0.589 11.975 0.004 −1.44110.533
GSTT1 glutathione
S-transferase theta 1 NM_008185 0.0130.5912.7910.026−0.502 13.293 0.001 −1.092 12.201
HMGCS2
3-hydroxy-3-
methylglutaryl-
Coenzyme A synthase
2 (mitochondrial)
NM_008256 0.0061.25711.845 0.0310.868 10.978 0.258 −0.39 10.588
IL1R2 interleukin 1
receptor, type II NM_010555 0.002−1.4532.7190.3180.305 2.413 0.001 1.7594.172
MAOB monoamine oxidase B NM_172778 0.0380.46312.20.035−0.473 12.673 0.002 −0.93611.737
MAP2K7 mitogen-activated
protein kinase kinase 7 NM_0010425570.1140.613 4.4990.2710.348 3.444 0.032
−0.912 3.887
NR1H4
nuclear receptor
subfamily 1, group
H, member 4
NM_009108 0.0420.5735.1430.183−0.337 5.48 0.006 −0.91 4.57
PAPSS2
3'-phosphoadenosine
5'-phosphosulfate
synthase 2
NM_011864 0.0020.52611.3380.007−0.403 11.74 0 −0.92810.812
SLC27A1
solute carrier family 27
(fatty acid transporter),
member 1
NM_011977 0.0040.813 11.7680.0160.619 11.149 0.342 −0.19410.955
SULT1A1
sulfotransferase family,
cytosolic, 1A,
phenol-preferring,
member 1
NM_133670 0.0540.63513.7090.529−0.179 13.888 0.022 −0.81413.073
SULT1E1
sulfotransferase family
1E, estrogen-preferring,
member 1
NM_023135 0.0560.44610.5030.004−0.856 11.36 0 −1.30310.057
TNFRSF11B
tumor necrosis factor
receptor superfamily,
member 11b
(osteoprotegerin)
NM_008764 0.1470.5256.2 0.075−0.675 6.875 0.008 −1.2 5.675
G-Protein Coupled Receptor Signaling
ADCY7 adenylate cyclase 7 NM_0010377230.08−0.75810.6450.2040.467 7.078 0.019 1.034 8.113
ADRB3 adrenergic, beta-3-,
receptor NM_013462 0.0181.98112.716 0.733 −0.187 13.423 0.012 −1.83 11.592
BCL3 B-cell CLL/lymphoma 3 NM_033601 0.03−0.3928.2810.0020.684 7.596 0 1.0768.672
CAMK2D
calcium/calmodulin-
dependent protein kinase
(CaM kinase) II delta
NM_0010254380.062 0.0872.365 0.496 −0.25 7.43 0.038 −0.902 6.528
DUSP9 dual specificity
phosphatase 9 NM_029352 0.446−0.3084.250.0072.199 3.445 0.005 2.294 5.74
HTR2B 5-hydroxytryptamine
(serotonin) receptor 2B NM_008311 0.022−3.2443.063 0.4770.81 2.252 0.008 4.0556.307
IKBKE
inhibitor of kappa light
polypeptide gene enhancer
in B-cells, kinase epsilon
NM_019777 0.013−0.5558.5310.0290.456 8.075 0.001 1.012 9.086
P2RY1 purinergic receptor P2Y,
G-protein coupled, 1 NM_008772 0.017−0.5137.3030 1.407 5.895 0 1.927.816

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 77
Continued
P2RY6 pyrimidinergic receptor
P2Y, G-protein coupled, 6 NM_183168 0.047−0.8211.1710.1690.518 10.653 0.006 1.338 11.991
PDE1A
phosphodiesterase
1A, calmodulin-
dependent
NM_001009978 0.0031.2398.6990.059 −0.608 9.306 0 −1.847 7.46
PDE2A phosphodiesterase 2A,
cGMP-stimulated NM_001008548 0.148−0.25210.0920.0040.683 9.41 0.001
0.935 10.345
PDE4B
phosphodiesterase 4B,
cAMP-specific
(phosphodiesterase E4
dunce homolog, Drosophila)
NM_019840 0 1.1048.990.001 0.883 8.107 0.222 −0.222 7.885
PDE7A phosphodiesterase 7A NM_001122759 0.14−0.4368.998 0.003 1.237 8.55 0.001 1.448 9.997
PDE8B phosphodiesterase 8B NM_172263 0.043−1.0833.1460.8030.111 3.035 0.03 1.1944.229
PIK3CA phosphoinositide-3-kinase,
catalytic, alpha polypeptide NM_008839 0.0010.6456.7550.127−0.249 7.833 0 −0.815 6.11
PIK3CD phosphoinositide-3-kinase,
catalytic, delta polypeptide NM_001029837 0.053−0.5486.2160.256 −0.386 9.26 0.012
0.813 6.764
PIK3R1 phosphoinositide-3-kinase,
regulatory subunit 1 (alpha) NM_001024955 0.0090.628 9.6450.001−0.697 13.043 0 −1.402 9.017
PIK3R3 phosphoinositide-3-kinase,
regulatory subunit 3 (gamma) NM_181585 0.281−0.2867.8270.060.555 7.271 0.012
0.841 8.112
PIK3R5 phosphoinositide-3-kinase,
regulatory subunit 5 NM_177320 0.155−0.6927.330.022 1.299 6.031 0.003 1.991 8.022
PLCB4 phospholipase C, beta 4 NM_013829 0.0151.0364.2860.28−0.212 10.733 0.01 −1.154 3.251
RGS18 regulator of G-protein
signaling 18 NM_022881 0.026−0.8159.1060.6290.151 8.392 0.016 0.9159.921
RGS2 regulator of G-protein
signaling 2, 24 kDa NM_009061 0.02−1.287.6990.3370.422 9.278 0.007 1.42 10.466
RGS4 regulator of G-protein
signaling 4 NM_009062 0.0041.0136.6330.0740.496 6.137 0.065 −0.517 5.619
TR/RXR Activation
ACACA acetyl-Coenzyme A
carboxylase alpha NM_133360 0.9120.0643.1130.009−2.07 5.182 0.008 −2.134 3.048
BCL3 B-cell CLL/lymphoma 3 NM_033601 0.03−0.3928.2810.0020.684 7.596 0 1.076 8.672
F10 coagulation factor X NM_007972 0.11−0.3153.270.002 1.908 6.065 0 1.2013.585
FRAP1
FK506 binding protein
12-rapamycin
associated protein 1
NM_020009 0.05−0.8254.1570.274 −0.144 10.371 0.031 0.938 4.981
KLF9 Kruppel-like factor 9 NM_010638 0.0030.55212.6060.002−0.476 13.011 0 −0.861 12.15
LDLR
low density lipoprotein
receptor (familial
hypercholesterolemia)
NM_010700 0 −0.9289.280.237 −0.036 3.487 0 0.9 10.207
NCOR1 nuclear receptor
co-repressor 1 NM_011308 0.0020.8648.3330.039 −0.595 5.03 0.001 −1.134 7.47
PCK1
phosphoenolpyruvate
carboxykinase 1
(soluble)
NM_011044 0.0022.19312.8270.7830.181 12.921 0.002 −2.22910.633
PIK3CA
phosphoinositide-
3-kinase, catalytic,
alpha polypeptide
NM_008839 0.0010.6456.7550.127−0.249 7.833 0 −0.815 6.11

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 78
Continued
PIK3CD
phosphoinositide-3-
kinase, catalytic,
delta polypeptide
NM_0010298370.053−0.5486.2160.256 −0.386 9.26 0.012 0.813 6.764
PIK3R1
phosphoinositide-3-
kinase, regulatory
subunit 1 (alpha)
NM_0010249550.0090.6289.6450.001 −0.697 13.043 0 −1.4029.017
PIK3R3
phosphoinositide-3-
kinase, regulatory
subunit 3 (gamma)
NM_181585 0.281−0.2867.8270.060.555 7.271 0.012 0.841 8.112
PIK3R5
phosphoinositide-3-
kinase, regulatory
subunit 5
NM_177320 0.155−0.6927.330.022 1.299 6.031 0.003 1.991 8.022
THRA
thyroid hormone receptor,
alpha (erythroblastic
leukemia viral
(v-erb-a) oncogene
homolog, avian)
NM_178060 0.0110.49611.440.007−0.551 11.991 0 −1.047 10.944
UCP2
uncoupling protein
2 (mitochondrial,
proton carrier)
NM_011671 0.056−0.53312.5980.0090.836 11.761 0.001 1.369 13.13
Sonic Hedgehog Signaling
C2 complement component 2 NM_013484 0.0050.85912.6560.057 −0.441 14.039 0.001 −1.319 11.797
C3AR1 complement component
3a receptor 1 NM_009779 0.037−1.01711.9030.0621.088 10.166 0.003 1.917 11.113
C5AR1 complement component
5a receptor 1 NM_008555 0.996−0.0023.6310.012−1.298 4.929 0.012 −1.296 3.633
CCNB1 cyclin B1 NM_007577 0.094−0.8018.2310.0720.665 9.86 0.011 1.095 10.955
CDC2 cell division cycle 2,
G1 to S and G2 to M NM_0010811250.61 −0.1093.3130.019−1.043 7.217 0.011 −1.2 6.017
GLI2 GLI-Kruppel family
member GLI2 NM_172301 0.026−1.5715.055 0.0641.214 3.841 0.002 2.785 6.626
MASP1
mannan-binding lectin
serine peptidase 1
(C4/C2 activating
component of
Ra-reactive factor)
NM_007659 0.013−1.3958.3420.021.253 7.088 0 2.648 9.736
Cell Cycle: G1/S Checkpoint Regulation
CCNE1 cyclin E1 NM_007633 0.071−0.6717.7280.140.523 7.205 0.008 1.194 8.398
CDK6 cyclin-dependent kinase 6 NM_009873 0.024−0.7629.0290.0930.629 7.834 0.003 1.211 9.791
CDKN1A cyclin-dependent kinase
inhibitor 1A (p21, Cip1) NM_0011110990.026 −0.6799.893 0.0011.468 8.425 0 2.146 10.571
CDKN1B cyclin-dependent kinase
inhibitor 1B (p27, Kip1) NM_009875 0.1250.398.6960.093−0.436 9.132 0.009
−0.826 8.306
CDKN2B
cyclin-dependent kinase
inhibitor 2B
(p15, inhibits CDK4)
NM_007670 0 −1.0139.990.8350.032 9.957 0 1.045 11.003
E2F1 E2F transcription factor 1 NM_007891 0.085−0.3546.9770.0160.663 8.141 0.002 0.904 7.331
E2F6 E2F transcription factor 6 NM_033270 0.009−1.1627.857 0.0141.06 6.797 0 2.222 9.019
HDAC11 histone deacetylase 11 NM_144919 0.0150.8256.4160.229−0.036 2.48 0.017 −0.8 5.59

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 79
Continued
HDAC9 histone deacetylase 9 NM_024124 0.11−0.4618.3630.1310.43 7.933 0.011 0.891 8.824
RB1
retinoblastoma 1
(including
osteosarcoma)
NM_009029 0.038−0.654.4830.0980.483 4.001 0.003 1.133 5.134
SKP2
S-phase kinase-
associated protein
2 (p45)
NM_013787 0.214−0.5993.8760.1380.737 3.139 0.02 1.337 4.476
TGFB3 transforming growth
factor, beta 3 NM_009368 0.0010.49510.6690.009−0.337 11.006 0 −0.832 10.174
GM-CSF Signaling
BCL2A1 BCL2-related protein A1 NM_007534 0.11−0.78410.911 0.0580.973 9.938 0.005 1.756 11.694
CAMK2D
calcium/calmodulin-
dependent protein
kinase (CaM kinase)
II delta
NM_0010254380.062 0.0872.3650.496−0.25 7.43 0.038 −0.902 6.528
HCK hemopoietic cell kinase NM_010407 0.016−0.9649.8790.0630.663 9.216 0.001 1.627 10.843
LYN
v-yes-1 Yamaguchi
sarcoma viral related
oncogene homolog
NM_0011110960.047 −0.51610.2230.2110.291 9.933 0.008
0.806 10.739
PIK3CA phosphoinositide-3-kinase,
catalytic, alpha polypeptide NM_008839 0.0010.6456.7550.127−0.249 7.833 0 −0.815 6.11
PIK3CD phosphoinositide-3-kinase,
catalytic, delta polypeptide NM_0010298370.053 −0.5486.2160.256 −0.386 9.26 0.012
0.813 6.764
PIK3R1 phosphoinositide-3-kinase,
regulatory subunit 1 (alpha) NM_0010249550.0090.6289.6450.001 −0.697 13.043 0 −1.4029.017
PIK3R3 phosphoinositide-3-kinase,
regulatory subunit 3 (gamma) NM_181585 0.281−0.2867.8270.060.555 7.271 0.012
0.841 8.112
PIK3R5 phosphoinositide-3-kinase,
regulatory subunit 5 NM_177320 0.155−0.6927.330.0221.299 6.031 0.003 1.991 8.022
PIM1 pim-1 oncogene NM_008842 0.032−1.33.5450.4590.18 8.558 0.06 1.086 4.845
RUNX1
runt-related transcription
factor 1 (acute myeloid
leukemia 1; aml1 oncogene)
NM_0011110210.024 −0.8124.6220.2460.506 4.344 0.01 1.447 5.791
LXR/RXR Activation
ABCG1
ATP-binding cassette,
sub-family G (WHITE),
member 1
NM_009593 0.097−0.53511.624 0.0220.827 10.798 0.002 1.361 12.159
ACACA acetyl-Coenzyme A
carboxylase alpha NM_133360 0.9120.0643.1130.009−2.07 5.182 0.008 −2.1343.048
APOC2 apolipoprotein C-II NM_009695 0.187−0.449.3160.0730.639 8.677 0.01 1.08 9.756
APOC4
(includes EG:346) apolipoprotein C-IV NM_007385 0 −2.2482.1260.9960.001 2.125 0 2.249 4.375
CCL7 chemokine (C-C motif)
ligand 7 NM_013654 0.009−1.62610.3110.0081.689 8.623 0 3.314 11.937
IL1R2 interleukin 1 receptor,
type II NM_010555 0.002−1.4532.7190.3180.305 2.413 0.001 1.759 4.172
IL1RN interleukin 1 receptor
antagonist NM_0010397010.005 −1.8052.2030 3.3 3.963 0 4.59 8.553
LDLR
low density lipoprotein
receptor (familial
hypercholesterolemia)
NM_010700 0 −0.9289.280.237 −0.036 3.487 0 0.9 10.207

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 80
Continued
MMP9
matrix metallopeptidase
9 (gelatinase B, 92 kDa
gelatinase, 92 kDa type
IV collagenase)
NM_013599 0.0812.2657.7870.268 −1.057 9.127 0.019 −3.4115.522
MSR1 macrophage scavenger
receptor 1 NM_0011133260.027 −0.9722.914 0.0091.537 4.507 0.001 1.778 10.468
NCOR1 nuclear receptor
co-repressor 1 NM_011308 0.0020.8648.3330.039 −0.595 5.03 0.001 −1.134 7.47
TNFRSF11B
tumor necrosis factor
receptor superfamily,
member 11b
(osteoprotegerin)
NM_008764 0.1470.5256.2 0.075−0.675 6.875 0.008 −1.2 5.675
Eicosanoid Signaling
ALOX15 arachidonate
15-lipoxygenase NM_009660 0.2110.6948.6420.154−0.808 9.45 0.022 −1.5017.949
FPRL1
(includes EG:2358) formyl peptide receptor 2 NM_008039 0.266−0.3466.0490.1040.539 5.51 0.019
0.885 6.396
LAMB2 laminin, beta 2 (laminin S) NM_008483 0.0270.6087.6770.346−0.215 7.893 0.007 −0.8247.069
PGDS prostaglandin D2
synthase, hematopoietic NM_019455 0.112−1.7157.268 0.1031.77 5.498 0.009 3.485 8.984
PLA2G2D phospholipase A2, group IID NM_011109 0.0911.3387.4130.107 −1.261 8.674 0.007 −2.66.075
PLA2G2E phospholipase A2, group IIE NM_012044 0.229−0.45410.0540.0041.54 8.514 0.001 1.993 10.508
PLA2G5 phospholipase A2, group V NM_0011229540.039−1.493.435 0.0941.126 2.309 0.003 2.615 4.924
PNPLA3 patatin-like phospholipase
domain containing 3 NM_054088 0.3090.3519.1540.157−0.51 9.663 0.033
−0.861 8.803
PTGER2 prostaglandin E receptor
2 (subtype EP2), 53 kDa NM_008964 0.159−0.4367.244 0.011 0.975 6.269 0.002 1.41 7.68
PTGER4 prostaglandin E receptor 4
(subtype EP4) AV230399 0.4640.1513.1210.0191.147 3.326 0.031 1.011 4.337
PTGES prostaglandin E synthase NM_022415 0.0441.00411.72 0.026 −1.15 9.87 0.007 −1.5910.716
PTGS1
prostaglandin-endoperoxide
synthase 1 (prostaglandin
G/H synthase and
cyclooxygenase)
NM_008969 0.0130.67410.6010.108−0.393 9.35 0.002 −0.969.927
TBXAS1
thromboxane A synthase
1 (platelet, cytochrome
P450, family 5, subfamily A)
NM_011539 0.095−0.414 10.70.023 0.63 10.07 0.002
1.044 11.113
WISP2 WNT1 inducible signaling
pathway protein 2 NM_016873 0.038−2.089.333 0.0043.495 5.837 0 5.576 11.413
YWHAZ
tyrosine 3-monooxygenase/
tryptophan 5-monooxygenase
activation protein,
zeta polypeptide
NM_011740 0.008−0.8767.2730.447 −0.188 7.461 0.024 0.6888.148
Coagulation System
F10 coagulation factor X NM_007972 0.11−0.3153.270.002 1.908 6.065 0 1.201 3.585
F2R coagulation factor II
(thrombin) receptor NM_010169 0.159−0.58710.4280.1160.669 9.76 0.013
1.256 11.015
F7
coagulation factor VII
(serum prothrombin
conversion accelerator)
NM_010172 0.232−1.26510.19 0.005 4.092 6.099 0.001 5.356 11.455

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 81
Continued
PLAUR plasminogen activator,
urokinase receptor NM_011113 0.009−0.4159.1510 0.855 8.296 0 1.27 9.565
SERPINA1
serpin peptidase inhibitor,
clade A (alpha-1
antiproteinase, antitrypsin),
member 1
NM_009243 0.002−1.0464.6530.2640.242 4.411 0 1.2885.699
SERPINE1
serpin peptidase inhibitor,
clade E (nexin, plasminogen
activator inhibitor type 1),
member 1
NM_008871 0.044−1.6158.7570.4030.578 8.179 0.013 2.19410.373
TFPI
tissue factor pathway
inhibitor (lipoprotein-
associated
coagulation inhibitor)
NM_011576 0.0450.7718.8770.004−0.514 9.297 0.002 −1.422 9.384
THBD thrombomodulin NM_009378 0.0010.77712.7510.001−0.829 13.58 0 −1.606 11.974
Aryl Hydrocarbon Receptor Signaling
ALDH3B1 aldehyde dehydrogenase
3 family, member B1 NM_026316 0.017−0.567.8480.0460.431 7.417 0.001
0.992 8.409
ALDH5A1
aldehyde dehydrogenase 5
family, member A1
(succinate-semialdehyde
dehydrogenase)
NM_172532 0.0120.80210.1080.459−0.18 10.288 0.004 −0.9829.306
ALDH6A1 aldehyde dehydrogenase 6
family, member A1 NM_134042 0.0020.50312.5660.009−0.359 12.925 0 −0.862 12.064
ARNT aryl hydrocarbon receptor
nuclear translocator NM_001037737 0.010.8316.1190.002 −0.259 8.705 0 −0.425 8.28
BAX BCL2-associated X protein NM_007527 0.033−0.45111.4660.0560.386 11.079 0.002 0.83711.917
CCNA2 cyclin A2 NM_009828 0.02−1.437.361 0.015 1.519 5.842 0.001 2.949 8.79
CCNE1 cyclin E1 NM_007633 0.071−0.6717.7280.140.523 7.205 0.008 1.194 8.398
CDK6 cyclin-dependent kinase 6 NM_009873 0.024−0.7629.0290.0930.629 7.834 0.003 1.211 9.791
CDKN1A cyclin-dependent kinase
inhibitor 1A (p21, Cip1) NM_001111099 0.026−0.6799.893 0.001 1.468 8.425 0 2.14610.571
CDKN1B cyclin-dependent kinase
inhibitor 1B (p27, Kip1) NM_009875 0.1250.398.6960.093−0.436 9.132 0.009
−0.826 8.306
E2F1 E2F transcription factor 1 NM_007891 0.085−0.3546.9770.0160.663 8.141 0.002 0.904 7.331
ESR1 estrogen receptor 1 NM_007956 0.0410.526.0970.033 −0.551 6.648 0.002 −1.071 5.577
FOS
v-fos FBJ murine
osteosarcoma viral
oncogene homolog
NM_010234 0.077−1.08910.7590.2070.725 10.034 0.012 1.81311.848
GSTA3 glutathione
S-transferase A3 NM_001077353 0.0610.95311.4150.127 −0.725 9.233 0.006 −1.6567.577
GSTA4 glutathione
S-transferase A4 NM_010357 0.040.85311.3860.122 −0.589 11.975 0.004 −1.441 10.533
GSTT1 glutathione
S-transferase theta 1 NM_008185 0.0130.5912.7910.026−0.502 13.293 0.001 −1.092 12.201
HSPB2 heat shock
27 kDa protein 2 NM_024441 0.003−0.8698.930.0830.393 8.537 0 1.262 9.799
NFIA nuclear factor I/A NM_001122952 0.0020.7996.2890.004−0.657 6.946 0 −1.456 5.49

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 82
Continued
NFKB2
nuclear factor of kappa
light polypeptide gene
enhancer in B-cells 2
(p49/p100)
NM_019408 0.3−0.2838.3790.0450.625 7.754 0.01 0.908 8.662
NR2F1 nuclear receptor subfamily
2, group F, member 1 NM_010151 0.0220.7445.6750.052−0.594 6.269 0.001 −1.3384.931
NRIP1 nuclear receptor interacting
protein 1 NM_173440 0.0020.67510.3560.004−0.572 10.928 0 −1.2479.681
RB1 retinoblastoma 1
(including osteosarcoma) NM_009029 0.038−0.654.4830.0980.483 4.001 0.003
1.133 5.134
TGFB3 transforming growth factor,
beta 3 NM_009368 0.0010.49510.6690.009−0.337 11.006 0 −0.83210.174
NFkB Signaling
BCL3 B-cell CLL/lymphoma 3 NM_033601 0.03−0.3928.2810.0020.684 7.596 0 1.076 8.672
BMP4 bone morphogenetic
protein 4 NM_007554 0.0041.21110.683 0.476 −0.209 10.892 0.002 −1.4219.471
CARD10 caspase recruitment
domain family, member 10 NM_130859 0.0060.72511.0390.286−0.209 11.248 0.002 −0.93410.315
CD40
CD40 molecule, TNF
receptor superfamily
member 5
NM_011611 0.005−0.6547.3440.1680.241 7.103 0.001 0.895 7.998
EGFR
epidermal growth factor
receptor (erythroblastic
leukemia viral (v-erb-b)
oncogene homolog, avian)
NM_007912 0.2510.4194.9920.095−0.381 9.611 0.024 −0.976 4.573
IL1R2 interleukin 1 receptor,
type II NM_010555 0.002−1.4532.7190.3180.305 2.413 0.001 1.759 4.172
IL1RN interleukin 1 receptor
antagonist NM_001039701 0.005−1.8052.2030 3.3 3.963 0 4.59 8.553
INSR insulin receptor NM_001033381 0 0.6689.9370.022−0.275 10.212 0 −0.9439.269
MAP2K7 mitogen-activated protein
kinase kinase 7 NM_001042557 0.1140.6134.4990.2710.348 3.444 0.032
−0.912 3.887
MAP3K3 mitogen-activated protein
kinase kinase kinase 3 NM_011947 0.049−2.0115.5490.137 −1.412 6.962 0.092 −0.237 9.719
NFKB2
nuclear factor of kappa
light polypeptide gene
enhancer in B-cells 2
(p49/p100)
NM_019408 0.3−0.2838.3790.0450.625 7.754 0.01 0.908 8.662
PIK3CA phosphoinositide-3-kinase,
catalytic, alpha polypeptide NM_008839 0.0010.6456.7550.127−0.249 7.833 0 −0.815 6.11
PIK3CD phosphoinositide-3-kinase,
catalytic, delta polypeptide NM_001029837 0.053−0.5486.2160.256 −0.386 9.26 0.012
0.813 6.764
PIK3R1 phosphoinositide-3-kinase,
regulatory subunit 1 (alpha) NM_001024955 0.0090.628 9.6450.001−0.697 13.043 0 −1.4029.017
PIK3R3 phosphoinositide-3-kinase,
regulatory subunit 3 (gamma) NM_181585 0.281−0.2867.8270.060.555 7.271 0.012
0.841 8.112
PIK3R5 phosphoinositide-3-kinase,
regulatory subunit 5 NM_177320 0.155−0.6927.330.022 1.299 6.031 0.003 1.991 8.022
TLR1 toll-like receptor 1 NM_030682 0.043−1.2177.0190.1950.699 6.32 0.007 1.916 8.236
TLR7 toll-like receptor 7 NM_133211 0.083−0.7043.1970.4050.317 7.567 0.042
0.904 8.47
TLR8 toll-like receptor 8 NM_133212 0.048−1.5665.652 0.104 1.213 4.438 0.004 2.779 7.218

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 83
Continued
TNFRSF11A
tumor necrosis factor
receptor superfamily,
member 11a, NFKB
activator
NM_009399 0.046−0.8642.4890.3850.345 4.948 0.018 1.169 6.117
TNFRSF11B
tumor necrosis factor
receptor superfamily,
member 11b
(osteoprotegerin)
NM_008764 0.1470.5256.2 0.075−0.675 6.875 0.008 −1.2 5.675
TRA@ T cell receptor alpha
locus XM_0014715820.038 −1.4388.857 0.035 1.472 7.385 0.002 2.909 10.295
TRAF3 TNF receptor-associated
factor 3 NM_0010482060.046 −0.5623.9270.1460.376 3.551 0.005
0.939 4.489
TRAF5 TNF receptor-associated
factor 5 NM_011633 0.001−0.4637.5430 0.469 7.074 0 0.932 8.006
TRG@ T cell receptor gamma
locus NM_011558 0.2620.3963.9950.072−0.695 4.69 0.013
−1.09 3.599
IGF-1 Signaling
FOS
v-fos FBJ murine
osteosarcoma viral
oncogene homolog
NM_010234 0.077−1.08910.7590.2070.725 10.034 0.012 1.813 11.848
FOXO1 forkhead box O1 NM_019739 0.0070.656 10.7560.1−0.323 11.079 0.001 −0.979 10.1
IGF1R insulin-like growth
factor 1 receptor NM_010513 0.010.7458.2210.228−0.275 8.496 0.002
−1.019 7.476
IGFBP2 insulin-like growth factor
binding protein 2, 36 kDa NM_008342 0.0050.6016.2530
−1.694 7.948 0 −2.296 5.652
IRS1 insulin receptor substrate 1 NM_010570 0.0061.38711.258 0.089−0.681 11.939 0.001 −2.067 9.872
NEDD4
neural precursor cell
expressed,
developmentally
down-regulated 4
NM_010890 0 0.70912.250.006−0.107 12.357 0 −0.81611.541
NOV nephroblastoma
overexpressed gene NM_010930 0.0890.9017.8810.379 −0.424 8.306 0.024 −1.3266.98
PIK3CA phosphoinositide-3-kinase,
catalytic, alpha polypeptide NM_008839 0.0010.6456.7550.127−0.249 7.833 0 −0.8156.11
PIK3CD phosphoinositide-3-kinase,
catalytic, delta polypeptide NM_0010298370.053 −0.5486.2160.256 −0.386 9.26 0.012
0.813 6.764
PIK3R1 phosphoinositide-3-kinase,
regulatory subunit 1 (alpha) NM_0010249550.0090.6289.6450.001 −0.697 13.043 0 −1.402 9.017
PIK3R3 phosphoinositide-3-kinase,
regulatory subunit 3 (gamma) NM_181585 0.281−0.2867.8270.060.555 7.271 0.012
0.841 8.112
PIK3R5 phosphoinositide-3-kinase,
regulatory subunit 5 NM_177320 0.155−0.6927.330.0221.299 6.031 0.003 1.991 8.022
PRKCH protein kinase C, eta NM_008856 0.087−0.74310.472 0.0270.997 7.892 0.003 1.594 9.486
YWHAE
tyrosine 3-monooxygenase/
tryptophan 5-monooxygenase
activation protein, epsilon
polypeptide
BF714941 0.0121.2195.8740.053−0.267 8.76 0.003 −1.598 4.655
YWHAZ
tyrosine 3-monooxygenase/
tryptophan 5-monooxygenase
activation protein,
zeta polypeptide
NM_011740 0.008−0.8767.2730.447 −0.188 7.461 0.024 0.6888.148
Fc Epsilon RI Signaling

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 84
Continued
BTK Bruton agammaglobulinemia
tyrosine kinase NM_013482 0.009−1.0579.3760.6070.153 9.223 0.005 1.21 10.433
FCER1A
Fc fragment of IgE, high
affinity I, receptor for; alpha
polypeptide
NM_010184 0.05−1.0437.4850.8080.109 7.375 0.035 1.152 8.528
FCER1G
Fc fragment of IgE, high
affinity I, receptor for;
gamma polypeptide
NM_010185 0.032−0.57314.1570.2560.26 13.897 0.006 0.833 14.73
LCP2
lymphocyte cytosolic protein
2 (SH2 domain containing
leukocyte protein of 76 kDa)
NM_010696 0.082−0.3629.4480.030.488 8.96 0.002 0.85 9.809
LYN v-yes-1 Yamaguchi sarcoma
viral related oncogene homolog NM_0011110960.047 −0.51610.2230.2110.291 9.933 0.008
0.806 10.739
MAP2K7 mitogen-activated protein
kinase kinase 7 NM_0010425570.1140.613 4.4990.2710.348 3.444 0.032
−0.912 3.887
MAPK14 mitogen-activated protein
kinase 14 NM_011951 0.0020.8467.580.062−0.064 12.45 0 −0.194 12.256
PIK3CA phosphoinositide-3-kinase,
catalytic, alpha polypeptide NM_008839 0.0010.6456.7550.127−0.249 7.833 0 −0.8156.11
PIK3CD phosphoinositide-3-kinase,
catalytic, delta polypeptide NM_0010298370.053 −0.5486.2160.256−0.386 9.26 0.012
0.813 6.764
PIK3R1 phosphoinositide-3-kinase,
regulatory subunit 1 (alpha) NM_0010249550.0090.6289.6450.001 −0.697 13.043 0 −1.402 9.017
PIK3R3 phosphoinositide-3-kinase,
regulatory subunit 3 (gamma) NM_181585 0.281−0.2867.8270.060.555 7.271 0.012
0.841 8.112
PIK3R5 phosphoinositide-3-kinase,
regulatory subunit 5 NM_177320 0.155−0.6927.330.022 1.299 6.031 0.003 1.9918.022
PLA2G2D phospholipase A2, group IID NM_011109 0.0911.3387.4130.107−1.261 8.674 0.007 −2.6 6.075
PLA2G2E phospholipase A2, group IIE NM_012044 0.229−0.45410.054 0.0041.54 8.514 0.001 1.993 10.508
PLA2G5 phospholipase A2, group V NM_0011229540.039−1.493.4350.0941.126 2.309 0.003 2.6154.924
PRKCH protein kinase C, eta NM_008856 0.087−0.74310.472 0.0270.997 7.892 0.003 1.5949.486
PRKD1 protein kinase D1 NM_008858 0 0.37710.7130 −0.515 11.227 0 −0.892 10.336
VAV1 vav 1 guanine nucleotide
exchange factor NM_011691 0.044−0.7045.7550.2090.391 5.363 0.007
1.095 6.458
VAV3 vav 3 guanine nucleotide
exchange factor NM_020505 0.072−0.7688.7430.1160.582 3.591 0.009
1.336 9.51
B Cell Receptor Signaling
BCL2A1 BCL2-related protein A1 NM_007534 0.11−0.78410.911 0.0580.973 9.938 0.005 1.75611.694
BCL3 B-cell CLL/lymphoma 3 NM_033601 0.03−0.3928.2810.0020.684 7.596 0 1.0768.672
BLNK B-cell linker NM_008528 0.054−1.111 11.9960.090.942 11.054 0.004 2.053 13.107
BTK Bruton agammaglobulinemia
tyrosine kinase NM_013482 0.009−1.0579.3760.6070.153 9.223 0.005 1.21 10.433
CAMK2D
calcium/calmodulin-dependent
protein kinase (CaM kinase)
II delta
NM_0010254380.0620.0872.365 0.496 −0.25 7.43 0.038 −0.902 6.528
CARD10 caspase recruitment domain
family, member 10 NM_130859 0.0060.72511.0390.286−0.209 11.248 0.002 −0.934 10.315

J. Tseng-Crank et al. / Open Journal of Genetics 3 (2013) 9-86 85
Continued
FCGR2A Fc fragment of IgG, low
affinity IIa, receptor (CD32) NM_010188 0.051−0.46712.20.1250.343 11.857 0.005 0.8112.667
FRAP1
FK506 binding protein
12-rapamycin associated
protein 1
NM_020009 0.05−0.8254.1570.274−0.144 10.371 0.031 0.9384.981
IKBKE
inhibitor of kappa light
polypeptide gene enhancer
in B-cells, kinase epsilon
NM_019777 0.013−0.5558.5310.0290.456 8.075 0.001 1.012 9.086
LYN v-yes-1 Yamaguchi sarcoma
viral related oncogene homolog NM_0011110960.047 −0.51610.2230.2110.291 9.933 0.008
0.806 10.739
MAP2K7 mitogen-activated protein
kinase kinase 7 NM_0010425570.1140.613 4.4990.2710.348 3.444 0.032
−0.912 3.887
MAP3K13 mitogen-activated protein
kinase kinase kinase 13 XM_0014808120.10.6764.220.4430 2.122 0.05
−0.853.543
MAP3K3 mitogen-activated protein
kinase kinase kinase 3 NM_011947 0.049−2.0115.5490.137−1.412 6.962 0.092 −0.2379.719
MAPK14 mitogen-activated protein
kinase 14 NM_011951 0.0020.8467.580.062−0.064 12.45 0 −0.194 12.256
PIK3AP1 phosphoinositide-3-kinase
adaptor protein 1 NM_031376 0.056−1.3866.5840.3120.652 5.932 0.013 2.038 7.97
PIK3CA phosphoinositide-3-kinase,
catalytic, alpha polypeptide NM_008839 0.0010.6456.7550.127−0.249 7.833 0 −0.815 6.11
PIK3CD phosphoinositide-3-kinase,
catalytic, delta polypeptide NM_0010298370.053 −0.5486.2160.256−0.386 9.26 0.012
0.813 6.764
PIK3R1 phosphoinositide-3-kinase,
regulatory subunit 1 (alpha) NM_0010249550.0090.6289.6450.001 −0.697 13.043 0 −1.4029.017
PIK3R3 phosphoinositide-3-kinase,
regulatory subunit 3 (gamma) NM_181585 0.281−0.2867.8270.060.555 7.271 0.012
0.841 8.112
PIK3R5 phosphoinositide-3-kinase,
regulatory subunit 5 NM_177320 0.155−0.6927.330.0221.299 6.031 0.003 1.991 8.022
VAV1 vav 1 guanine nucleotide
exchange factor NM_011691 0.044−0.7045.7550.2090.391 5.363 0.007
1.095 6.458
VAV3 vav 3 guanine nucleotide
exchange factor NM_020505 0.072−0.7688.7430.1160.582 3.591 0.009
1.336 9.51
Supplement Tables 1-4. Heatmaps in Supplement Fig-
ure 4 listed the pathways by rank order of statistical sig-
nificance.
span when sirtuin activity is heightened in response to
caloric restriction [11]. The similarity between UP780
and resveratrol was observed in both the highest differ-
ential gene expressions and in the significant metabolic
and signaling pathways. Resveratrol was discovered through
high throughput screening for sirtuin activation [11],
while UP780’s discovery was designed not to be specific
for enzymatic modification, but for increased adiponectin
secretion from differentiate 3T3-L1 adipocytes [1].
2.3. Comparison to Similar Microarray Data
Microarray results a few years ago were notorious for
data variability when comparing similar studies from dif-
ferent laboratories. To confirm our microarray result to
the published gene expression studies, two similar liver
microarray datasets from similar DIO mouse models [11,
12] were compared to our LC/LV/LUP dataset. Side-by-
side comparisons were remarkably similar. One dataset,
that of the resveratrol treated DIO model [11], was iden-
tical to our experimental design of lean control, HFD,
and HFD+resveratrol treatments. Not only were the com-
parisons between lean control and HFD similar, but also
the comparisons between LUP vs. LV and HFD + res-
veratrol vs. HFD similar. Resveratrol, a phenolic com-
pound from grape, activates sirtuin, a protein known
from yeast, Drosophila, and C. elegan to prolong life
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