Download Table S3

Supplementary Table 3. Selected genes in functional groups that are deregulated in liver of zebrafish
exposed to arsenic.
UniGene
Gene
(Build 79)
Gene Description
Difference Mean Log2 (Arsenic vs. Control)
symbol
*'Early'
** 'Late'
***'Overall'
2.33
Up-Regulated Genes
Heat Shock Proteins
Dr.11312
heat shock 10kD protein 1
hspe1
2.57
2.09
Dr.7108
heat shock 60kD protein 1
hspd1
4.15
3.14
3.64
Dr.24802
heat shock 70kDa protein 8
hspa8
1.00
2.75
1.87
Dr.20198
heat shock cognate 70-kd protein
hsp70
7.04
4.61
5.78
Dr.11431
heat shock protein 4
hspa4
0.81
1.24
1.00
Dr.5588
heat shock protein 4, like
hspa4l
3.44
1.41
2.39
Dr.610
heat shock protein 90-alpha
hsp90a
NS
2.21
1.33
Dr.31066
heat shock protein 90-beta
hsp90b
0.88
1.77
1.32
Dr.4503
heat shock protein 9B
hspa9b
2.16
3.09
2.79
Antioxidants
Dr.9770
peroxiredoxin 3
prdx3
NS
0.84
0.64
Dr.6314
superoxide dismutase 2, mitochondrial
sod2
1.79
3.18
2.48
Dr.7977
glutathione peroxidase 1
gpx1
1.55
3.03
2.29
Dr.24921
glutathione peroxidase 4b
gpx4b
NS
1.68
1.15
Dr.20170
APEX nuclease (multifunctional DNA repair enzyme) 1
1.16
Dr.36769
DNA excision repair protein ERCC-8
Dr.1378
growth arrest and DNA-damage-inducible, beta
Dr.33922
replication protein A2
Dr.14857
thyroid autoantigen 70kDa
Dr.28707
heme oxygenase 1
hmox1
2.32
NS
1.84
Dr.4829
aminolevulinate, delta-, synthetase 1
alas1
4.53
3.33
3.90
Dr.6496
ferritin, heavy polypeptide 1
fth1
2.52
3.44
2.98
Dr.9052
hypoxia-inducible factor 1
hif1a
0.66
1.48
1.16
Dr.17462
hypoxia up-regulated 1
hyou1
3.72
3.79
3.75
Dr.18233
metallothionein 2
mt2
3.32
3.21
3.26
Dr.7318
proteasome 26S subunit, ATPase 2
psmc2
2.14
NS
1.81
Dr.8213
proteasome subunit, beta type, 9b
psmb9b
1.88
1.13
1.47
Dr.20627
proteasome subunit, beta type, 5
psmb5
2.68
NS
2.27
Dr.10596
proteasome subunit, alpha type, 4
psma4
1.64
1.45
1.55
Dr.11843
proteasome subunit, beta type, 6
psmb6
1.20
1.59
1.43
Dr.15038
proteasome subunit, beta type, 1
psmb1
2.02
1.13
1.54
Dr.7957
proteasome subunit, beta type, 8
psmb8
NS
1.96
2.02
Dr.20872
proteasome subunit, alpha type, 6a
psma6a
NS
1.50
1.42
Dr.20156
proteasome subunit, alpha type, 5
psma5
2.09
1.56
1.93
Dr.19238
cathepsin D
ctsd
1.82
2.99
2.40
Dr.26555
cathepsin L, a
ctsla
1.20
1.94
1.57
Dr.2951
ubiquinol-cytochrome c reductase core protein II
uqcrc2
NS
1.13
0.78
Dr.28845
ubiquitin-activating enzyme E1
ube1
2.35
1.54
1.98
DNA Damage and Repair
apex
1.13
1.19
ercc-8
0.48
NS
0.44
gadd45b
1.12
1.70
1.41
rpa2
0.96
1.64
1.46
g22p1
0.58
NS
0.55
Oxidative Stress Inducible
Protein Catabolism
Dr.9101
ubiquitin-conjugating enzyme E2 variant 2
ube2v2
0.73
0.47
0.60
Dr.25785
ubiquitin-conjugating enzyme E2A (RAD6 homolog)
ube2a
0.79
0.78
0.77
Dr.20491
mahogunin, ring finger 1
mgrn1
NS
1.24
0.79
False Discovery Rate (FDR) < 0.5%
*'Early'
8h & 24h
False Discovery Rate (FDR) < 1%
** 'Late'
48h & 96h
False Discovery Rate (FDR) < 5%
***'Overall'
8h to 96h
NS
Not Significant (FDR > 5%)
Supplementary Table 3. (continued page 2)
UniGene
Gene
(Build 79)
Gene Description
symbol
Difference Mean Log2 (Arsenic vs. Control)
*'Early'
** 'Late'
***'Overall'
Up-Regulated Genes
Carbohydrate Catabolism and Energy
Dr.11244
glucose phosphate isomerase a
gpia
1.91
2.25
2.08
Dr.19225
aldolase a, fructose-bisphosphate
aldoa
1.86
2.32
2.06
Dr.20424
transaldolase 1
taldo1
1.76
1.61
1.66
Dr.729
lactate dehydrogenase B4
ldhb
1.36
0.92
1.14
Dr.898
phosphoglycerate kinase 1homolog (human)
pgk1
1.37
1.50
1.40
Dr.14669
UDP-glucose dehydrogenase
ugdh
2.55
1.12
1.83
Dr.11239
succinate dehydrogenase complex, subunit A
sdha
1.11
0.89
1.05
Dr.14189
dihydrodiol dehydrogenase (dimeric), like
dhdhl
2.95
1.30
2.12
Dr.10384
NADH dehydrogenase 1, alpha/beta subcomplex, 1
ndufab1
NS
1.82
1.06
Dr.7434
NADH dehydrogenase 1 beta subcomplex, 4
ndufb4
NS
0.73
0.41
Dr.6509
protein disulfide isomerase-related protein
pdip5
NS
2.16
1.93
Dr.9457
egl nine homolog 3 (C. elegans)
Dr.7906
cytochrome c oxidase subunit VIa polypeptide 1
Dr.4272
ATP synthase, H+ transporting, delta subunit
Dr.28209
egln3
2.70
2.30
2.50
coxVIa1
1.19
2.00
1.60
atp5d
NS
2.78
3.14
lysyl-tRNA synthetase
kars
1.37
2.45
1.93
Dr.20108
glutaminyl-tRNA synthetase
qars
NS
1.09
1.85
Dr.29078
seryl-tRNA synthetase
sars
1.23
1.16
1.16
Dr.1481
valyl-tRNA synthetase 2
vars2
0.43
0.73
0.58
Dr.9798
tyrosyl-tRNA synthetase
yars
3.01
2.38
2.69
Dr.1961
ribosomal protein L7-like 1
rpl7l1
2.08
1.22
1.66
Dr.3421
ribosome binding protein 1 homolog (dog)
rrbp1
1.55
1.98
1.77
Dr.7787
ribosomal protein S27-like
rps27l
2.42
2.12
2.27
Dr.25507
eukaryotic translation initiation factor 2, subunit 2 beta
eif2s2
0.98
1.20
1.06
Dr.24841
eukaryotic translation initiation factor 4A, isoform 1A
eif4a1a
1.22
NS
0.89
Dr.24582
eukaryotic translation initiation factor 2 subunit 1 alpha like
eif2s1l
NS
0.80
0.58
Dr.26653
eukaryotic translation initiation factor 2 subunit 3 gamma
eif2s3
NS
NS
0.67
Dr.1142
dolichyl-diphosphooligosaccharide-protein glycosyltransferase
ddost
NS
1.67
1.07
Dr.4217
ribophorin II
rpn2
NS
2.01
1.19
Dr.445
ribophorin I
rpn1
NS
1.95
1.21
Dr.11244
glucose phosphate isomerase a
gpia
1.91
2.25
2.08
pc
3.04
4.41
3.73
has2
NS
1.72
1.13
Protein Biosynthesis
Glycoprotein and Carbohydrate Biosynthesis
Dr.5998
pyruvate carboxylase
Dr.10465
hyaluronan synthase 2
Dr.23788
glutathione S-transferase pi
gstp1
3.01
3.61
3.31
Dr.16014
glutathione S-transferase omega 1
gsto1
2.67
NS
1.57
Dr.22620
glutathione S-transferase, theta 3
Dr.879
HMT1 hnRNP methyltransferase-like 2
Dr.1867
spermine synthase
Dr. 43156
methionine adenosyltransferase 2 alpha
Dr.18396
thioredoxin interacting protein
Dr.25282
thioredoxin reductase 1
Dr.31444
thioredoxin
Dr.18739
thioredoxin-like 1
Arsenic Metabolism
False Discovery Rate (FDR) < 0.5%
NS
gstt3
2.89
4.28
3.58
hrmt1l2
2.33
1.65
2.13
sms
1.00
1.19
1.13
mat2a
NS
1.04
0.90
txnip
NS
1.46
0.86
txnrd1
2.15
1.73
2.04
tx
3.27
3.58
3.42
txl1
2.51
1.67
2.10
*'Early'
8h & 24h
False Discovery Rate (FDR) < 1%
** 'Late'
48h & 96h
False Discovery Rate (FDR) < 5%
***'Overall'
8h to 96h
Not Significant (FDR > 5%)
Supplementary Table 3. (continued page 3)
UniGene
Gene
(Build 79)
Gene Description
Difference Mean Log2 (Arsenic vs. Control)
symbol
*'Early'
** 'Late'
***'Overall'
Up-Regulated Genes
Transportation
Dr.1519
RAB6A, member RAS oncogene family
rab6a
1.17
0.76
0.97
Dr.7401
RAB5A, member RAS oncogene family
rab5a
1.54
1.42
1.56
Dr.4874
RAB1A, member RAS oncogene family
rab1a
NS
1.45
1.63
Dr.12260
RAB7, member RAS oncogene family
rab7
NS
0.42
0.37
Dr.20914
RAB2, member RAS oncogene family
rab2
0.70
3.01
1.76
Dr.7872
RAB14, member RAS oncogene family
rab14
NS
1.30
0.79
Dr.13128
RAB11A, member RAS oncogene family
rab11a
0.96
1.26
1.03
Dr.1915
RAB11B, member RAS oncogene family
rab11b
0.68
0.59
0.63
Dr.14855
RAB35, member RAS oncogene family
rab35
NS
0.36
0.41
Dr.321
ras-related nuclear protein
ran
0.95
0.36
0.65
Dr.2921
coatomer protein complex, subunit alpha
copa
0.70
0.83
0.77
1.61
Dr.6631
KDEL endoplasmic reticulum protein retention receptor 2
Dr.12521
translocase of outer mitochondrial membrane 20
kdelr2
0.85
2.54
tomm20
1.07
1.72
Dr.7990
signal recognition particle 54kDa
1.40
srp54
1.11
1.42
1.26
Dr.1209
signal sequence receptor, beta
ssr2
NS
0.95
0.81
Dr.297
signal sequence receptor, gamma homolog
ssr3
NS
1.39
0.98
Dr.34881
ATP-binding cassette, sub-family C member 4
Dr.10719
ATPase, Na+/K+ transporting, alpha 1a.4 polypeptide
Dr.8148
Dr.28281
abcc4
NS
1.62
1.12
atp1a1a.4
1.12
2.45
1.78
catenin alpha
ctnna
1.26
1.14
1.24
beta-catenin 2
ctnnb2
NS
0.71
0.52
Cell Adhesion and Cytoskeletal Reorganization
Dr.5605
tubulin, beta, 2
tubb2
2.44
2.21
2.32
Dr.28850
tubulin, alpha 8 like
tuba8l
3.15
2.61
2.90
Dr.664
tubulin, alpha 8 like 4
tuba8l4
2.85
1.62
2.27
Dr.25213
beta actin 1
bactin1
2.82
1.92
2.34
Dr.1109
beta actin 2
bactin2
NS
1.72
1.10
Dr.1282
keratin 8
krt8
2.00
3.54
2.77
Dr.28198
cofilin 2 like
cfl2l
NS
1.88
1.35
Dr.28419
profilin 2 like
pfn2l
0.85
0.95
0.91
Dr.20954
kinesin 2
kns2
NS
1.53
0.99
Dr.3027
erythrocyte membrane protein band 4.1 (elliptocytosis 1)
epb41
0.40
0.29
0.34
0.92
Miscellaneous
Dr.8151
signal transduction and activation of transcription 1
stat1
NS
1.14
Dr.275
janus kinase 1
jak1
1.05
1.41
1.23
Dr.4711
ras-related C3 botulinum toxin substrate 1
rac1
1.26
1.36
1.37
Dr.1212
cyclin G1
Dr.25777
mitogen-activated protein kinase-activated protein kinase 2
ccng1
1.15
3.25
2.20
mapkapk2
1.13
NS
0.87
0.91
Dr.4957
myeloid cell leukemia sequence 1a
mcl1a
1.00
0.78
Dr.10465
hyaluronan synthase 2
has2
NS
1.72
1.13
Dr.12605
cyclin-dependent kinase inhibitor 1b
cdkn1b
0.99873
NS
0.88209
False Discovery Rate (FDR) < 0.5%
NS
*'Early'
8h & 24h
False Discovery Rate (FDR) < 1%
** 'Late'
48h & 96h
False Discovery Rate (FDR) < 5%
***'Overall'
8h to 96h
Not Significant (FDR > 5%)
Supplementary Table 3. (continued page 4)
UniGene
Gene
(Build 79)
Gene Description
symbol
Difference Mean Log2 (Arsenic vs. Control)
*'Early'
** 'Late'
***'Overall'
Down-Regulated Genes
Blood Factors
Dr.1565
coagulation factor VII
f7
-1.07
NS
-0.74
Dr.19652
coagulation factor VIIi
f7i
-2.50
-2.18
-2.34
Dr.20017
coagulation factor IX
f9
-1.64
-1.40
-1.53
Dr.28864
serine (or cysteine) proteinase inhibitor, clade A member 1
serpina1
NS
-0.57
-0.43
Dr.4199
serine (or cysteine) proteinase inhibitor, clade C member 1
serpinc1
-1.89
NS
-1.27
Dr.356
GATA-binding protein 2
gata2
NS
-1.36
-1.46
Dr.10074
platelet-derived growth factor alpha polypeptide
pdgfa
NS
-0.92
-0.95
Dr.26356
hemoglobin alpha embryonic-1
hbae1
NS
-0.84
-0.88
Dr.12359
hydroxysteroid 11-beta dehydrogenase 2
hsd11b2
-3.26
-1.60
-2.49
Dr.12949
Deiodinase, iodothyronine, type II
dio2
-1.41
-1.49
-1.45
Dr.16113
inhibin, beta A
inhba
NS
-1.50
-1.40
Dr.15260
rev erb beta 2
reverbb2
NS
-1.59
-1.27
Dr.32157
Androgen receptor (dihydrotestosterone receptor)
ar
NS
-1.26
-1.07
Dr.11725
Estrogen receptor 2b
esr2b
NS
-1.13
-0.71
Dr.12402
insulin-like growth factor 1
igf1
NS
-1.07
-0.68
Dr.583
insulin promoter factor 1
ipf1
-0.73
-0.67
-0.70
Dr.4002
apolipoprotein B
apoB
-2.63
-1.27
-1.95
Dr.12241
carnitine palmitoyltransferase 1A
cpt1A
-2.24
-1.49
-1.87
slc27a3
-1.52
-2.21
-1.86
lpl
-2.28
NS
-1.32
Hormone-related Activity
Lipid Metabolism
Dr.4342
solute carrier family 27 (fatty acid transporter), member 3
Dr.20185
lipoprotein lipase
Dr.6814
fatty acid binding protein 3
fabp3
-0.74
-0.55
-0.65
Dr.3292
monoglyceride lipase
mgll
-1.42
NS
-0.79
Dr.20961
cytosolic phospholipase a2
cpla2
NS
-1.28
-0.88
Dr.742
transforming growth factor, beta-induced
Dr.563
spondin 2b
Dr.31832
Miscellaneous
tgfbi
-1.33
-1.45
-1.33
spon2b
NS
-1.90
-1.68
vimentin
vim
-0.67
-2.17
-1.55
Dr.24216
type I cytokeratin
cki
-0.72
-1.25
-0.99
Dr.1434
type II cytokeratin
ckii
NS
-0.66
-0.44
Dr.28593
retinol binding protein 1
rbp1
-2.47
NS
-2.22
Dr.409
fibroblast growth factor receptor 4
fgfr4
-1.90
-1.46
-1.70
Dr.25162
DNA (cytosine-5-)-methyltransferase 1
dnmt1
NS
-0.64
-0.41
Dr.12624
Iroquois homeobox protein 1, b
Dr.30528
homeo box D4a
Dr.14662
irx1b
NS
-1.96
-1.96
hoxd4a
NS
-1.93
-1.89
transcription factor 2, hepatic
tcf2
-0.92
NS
-0.68
Dr.18290
met proto-oncogene (hepatocyte growth factor receptor)
met
-0.49
-1.01
-0.75
Dr.608
musculoaponeurotic fibrosarcoma oncogene family, protein B
mafb
NS
-1.29
-1.13
False Discovery Rate (FDR) < 0.5%
NS
*'Early'
8h & 24h
False Discovery Rate (FDR) < 1%
** 'Late'
48h & 96h
False Discovery Rate (FDR) < 5%
***'Overall'
8h to 96h
Not Significant (FDR > 5%)