Rodrigues RR and CT Barry. Gene Pathway Analysis Of Hepatocellular Carcinoma Genomic Expression Datasets. Journal of Surgical Research, 170, e85-e92 (2011).

The following is the Master HCC Gene List from our analysis.

Symbol Entrez Gene Name
ACLY ATP citrate lyase
ACP1 acid phosphatase 1, soluble
ACTL6A actin-like 6A
ACTN4 actinin, alpha 4
ADAM10 ADAM metallopeptidase domain 10
ALG3 asparagine-linked glycosylation 3, alpha-1,3- mannosyltransferase homolog (S. cerevisiae)
ANLN anillin, actin binding protein
ANP32B acidic (leucine-rich) nuclear phosphoprotein 32 family, member B
ANXA2 annexin A2
AP3S1 adaptor-related protein complex 3, sigma 1 subunit
APEX1 APEX nuclease (multifunctional DNA repair enzyme) 1
ARHGAP12 Rho GTPase activating protein 12
ARID3A AT rich interactive domain 3A (BRIGHT-like)
ARMC1 armadillo repeat containing 1
ASPM asp (abnormal spindle) homolog, microcephaly associated (Drosophila)
ATAD2 ATPase family, AAA domain containing 2
ATP6V1F ATPase, H+ transporting, lysosomal 14kDa, V1 subunit F
AURKA aurora kinase A
AURKB aurora kinase B
BANF1 barrier to autointegration factor 1
BIRC5 baculoviral IAP repeat containing 5
BRP44 brain protein 44
BUB1 budding uninhibited by benzimidazoles 1 homolog (yeast)
BUB1B budding uninhibited by benzimidazoles 1 homolog beta (yeast)
BUB3 budding uninhibited by benzimidazoles 3 homolog (yeast)
CACYBP calcyclin binding protein
CANX calnexin
CAPNS1 calpain, small subunit 1
CAPZA2 capping protein (actin filament) muscle Z-line, alpha 2
CBX1 chromobox homolog 1
CCDC34 coiled-coil domain containing 34
CCDC99 coiled-coil domain containing 99
CCNA2 cyclin A2
CCNB1 cyclin B1
CCNB2 cyclin B2
CCT3 chaperonin containing TCP1, subunit 3 (gamma)
CCT4 chaperonin containing TCP1, subunit 4 (delta)
CCT5 chaperonin containing TCP1, subunit 5 (epsilon)
CCT6A chaperonin containing TCP1, subunit 6A (zeta 1)
CDC23 cell division cycle 23 homolog (S. cerevisiae)
CDC25B cell division cycle 25 homolog B (S. pombe)
CDC45 cell division cycle 45 homolog (S. cerevisiae)
CDC6 cell division cycle 6 homolog (S. cerevisiae)
CDC7 cell division cycle 7 homolog (S. cerevisiae)
CDCA2 cell division cycle associated 2
CDCA3 cell division cycle associated 3
CDCA5 cell division cycle associated 5
CDK1 cyclin-dependent kinase 1
CDK4 cyclin-dependent kinase 4
CDKN2A cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)
CDKN2C cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4)
CDKN3 cyclin-dependent kinase inhibitor 3
CENPE centromere protein E, 312kDa
CENPF centromere protein F, 350/400kDa (mitosin)
CENPL centromere protein L
CENPM centromere protein M
CGGBP1 CGG triplet repeat binding protein 1
CHEK1 CHK1 checkpoint homolog (S. pombe)
CHMP2A chromatin modifying protein 2A
CIT citron (rho-interacting, serine/threonine kinase 21)
CKAP2 cytoskeleton associated protein 2
CKAP4 cytoskeleton-associated protein 4
CKAP5 cytoskeleton associated protein 5
CKS1B CDC28 protein kinase regulatory subunit 1B
CKS2 CDC28 protein kinase regulatory subunit 2
CLIC1 chloride intracellular channel 1
COPB1 coatomer protein complex, subunit beta 1
COPS5 COP9 constitutive photomorphogenic homolog subunit 5 (Arabidopsis)
COX7A2L cytochrome c oxidase subunit VIIa polypeptide 2 like
CTNNA1 catenin (cadherin-associated protein), alpha 1, 102kDa
CUL4A cullin 4A
CYP2R1 cytochrome P450, family 2, subfamily R, polypeptide 1
DAP3 death associated protein 3
DDAH2 dimethylarginine dimethylaminohydrolase 2
DEK DEK oncogene
DIAPH3 diaphanous homolog 3 (Drosophila)
DNAJC9 DnaJ (Hsp40) homolog, subfamily C, member 9
DRAM2 DNA-damage regulated autophagy modulator 2
DRG1 developmentally regulated GTP binding protein 1
DTL denticleless homolog (Drosophila)
DVL3 dishevelled, dsh homolog 3 (Drosophila)
E2F1 E2F transcription factor 1
E2F8 E2F transcription factor 8
ECT2 epithelial cell transforming sequence 2 oncogene
EED embryonic ectoderm development
EFTUD2 elongation factor Tu GTP binding domain containing 2
EIF1AY eukaryotic translation initiation factor 1A, Y-linked
EIF2B1 eukaryotic translation initiation factor 2B, subunit 1 alpha, 26kDa
EIF2S2 eukaryotic translation initiation factor 2, subunit 2 beta, 38kDa
EIF5B eukaryotic translation initiation factor 5B
ENAH enabled homolog (Drosophila)
EPRS glutamyl-prolyl-tRNA synthetase
ESYT1 extended synaptotagmin-like protein 1
EXO1 exonuclease 1
EZH2 enhancer of zeste homolog 2 (Drosophila)
FADS1 fatty acid desaturase 1
FAM50A family with sequence similarity 50, member A
FANCG Fanconi anemia, complementation group G
FDPS farnesyl diphosphate synthase
FEN1 flap structure-specific endonuclease 1
FIBP fibroblast growth factor (acidic) intracellular binding protein
FLAD1 FAD1 flavin adenine dinucleotide synthetase homolog (S. cerevisiae)
FNBP1L formin binding protein 1-like
FOXM1 forkhead box M1
GARS glycyl-tRNA synthetase
GBF1 golgi brefeldin A resistant guanine nucleotide exchange factor 1
GCN1L1 GCN1 general control of amino-acid synthesis 1-like 1 (yeast)
GINS1 GINS complex subunit 1 (Psf1 homolog)
GLB1 galactosidase, beta 1
GMNN geminin, DNA replication inhibitor
GNPAT glyceronephosphate O-acyltransferase
GPC3 glypican 3
GPSM2 G-protein signaling modulator 2
GPX7 glutathione peroxidase 7
GTF2A2 general transcription factor IIA, 2, 12kDa
H2AFX H2A histone family, member X
H2AFZ H2A histone family, member Z
HAT1 histone acetyltransferase 1
HAX1 HCLS1 associated protein X-1
HCFC1 host cell factor C1 (VP16-accessory protein)
HDAC1 histone deacetylase 1
HDGF hepatoma-derived growth factor
HELLS helicase, lymphoid-specific
HMGA1 high mobility group AT-hook 1
HMGB2 high-mobility group box 2
HMGN4 high mobility group nucleosomal binding domain 4
HN1 hematological and neurological expressed 1
IARS isoleucyl-tRNA synthetase
IDI1 isopentenyl-diphosphate delta isomerase 1
IK IK cytokine, down-regulator of HLA II
ILF2 interleukin enhancer binding factor 2, 45kDa
ILF3 interleukin enhancer binding factor 3, 90kDa
IMPDH2 IMP (inosine 5′-monophosphate) dehydrogenase 2
INCENP inner centromere protein antigens 135/155kDa
INTS7 integrator complex subunit 7
ITGB3BP integrin beta 3 binding protein (beta3-endonexin)
KDELR1 KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 1
KIAA0101 KIAA0101
KIF11 kinesin family member 11
KIF14 kinesin family member 14
KIF20A kinesin family member 20A
KIF23 kinesin family member 23
KIF2C kinesin family member 2C
KIF4A kinesin family member 4A
KIF5B kinesin family member 5B
KIN KIN, antigenic determinant of recA protein homolog (mouse)
KNTC1 kinetochore associated 1
KPNA2 karyopherin alpha 2 (RAG cohort 1, importin alpha 1)
KPNB1 karyopherin (importin) beta 1
LBR lamin B receptor
LETM1 leucine zipper-EF-hand containing transmembrane protein 1
LGALS1 lectin, galactoside-binding, soluble, 1
LIG1 ligase I, DNA, ATP-dependent
LIG3 ligase III, DNA, ATP-dependent
LOC100287429/ZNF84 zinc finger protein 84
LPCAT1 lysophosphatidylcholine acyltransferase 1
LRRC59 leucine rich repeat containing 59
LSM4 LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae)
LTA4H leukotriene A4 hydrolase
MAD2L1 MAD2 mitotic arrest deficient-like 1 (yeast)
MANF mesencephalic astrocyte-derived neurotrophic factor
MAP3K7 mitogen-activated protein kinase kinase kinase 7
MAP4K4 mitogen-activated protein kinase kinase kinase kinase 4
MAPK6 mitogen-activated protein kinase 6
MAPKAPK5 mitogen-activated protein kinase-activated protein kinase 5
MARCKS myristoylated alanine-rich protein kinase C substrate
MAZ MYC-associated zinc finger protein (purine-binding transcription factor)
MCM3 minichromosome maintenance complex component 3
MCM4 minichromosome maintenance complex component 4
MCM6 minichromosome maintenance complex component 6
MCM7 minichromosome maintenance complex component 7
MCM7 minichromosome maintenance complex component 7
MDK midkine (neurite growth-promoting factor 2)
MELK maternal embryonic leucine zipper kinase
MESDC2 mesoderm development candidate 2
MGAT4B mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme B
MKI67 antigen identified by monoclonal antibody Ki-67
MLF1IP MLF1 interacting protein
MORF4L2 mortality factor 4 like 2
MRPL13 mitochondrial ribosomal protein L13
MRPL3 mitochondrial ribosomal protein L3
MRPL45 mitochondrial ribosomal protein L45
MRPS12 mitochondrial ribosomal protein S12
MRPS14 mitochondrial ribosomal protein S14
MSH2 mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)
MSH6 mutS homolog 6 (E. coli)
MYBL2 v-myb myeloblastosis viral oncogene homolog (avian)-like 2
NAB2 NGFI-A binding protein 2 (EGR1 binding protein 2)
NCAPG non-SMC condensin I complex, subunit G
NCAPG2 non-SMC condensin II complex, subunit G2
NDUFB3 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 3, 12kDa
NEDD8 neural precursor cell expressed, developmentally down-regulated 8
NEK2 NIMA (never in mitosis gene a)-related kinase 2
NHP2L1 NHP2 non-histone chromosome protein 2-like 1 (S. cerevisiae)
NME1 non-metastatic cells 1, protein (NM23A) expressed in
NME2 non-metastatic cells 2, protein (NM23B) expressed in
NOMO1 (includes others) NODAL modulator 1
NONO non-POU domain containing, octamer-binding
NOP56 NOP56 ribonucleoprotein homolog (yeast)
NPEPPS aminopeptidase puromycin sensitive
NSD1 nuclear receptor binding SET domain protein 1
NUCKS1 nuclear casein kinase and cyclin-dependent kinase substrate 1
NUDT1 nudix (nucleoside diphosphate linked moiety X)-type motif 1
NUP205 nucleoporin 205kDa
NUP214 nucleoporin 214kDa
NUP85 nucleoporin 85kDa
NUSAP1 nucleolar and spindle associated protein 1
OGT O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)
OLIG2 oligodendrocyte lineage transcription factor 2
ORC1 origin recognition complex, subunit 1
PA2G4 proliferation-associated 2G4, 38kDa
PARP1 poly (ADP-ribose) polymerase 1
PBK PDZ binding kinase
PCNA proliferating cell nuclear antigen
PDCD5 programmed cell death 5
PEA15 phosphoprotein enriched in astrocytes 15
PGK1 phosphoglycerate kinase 1
PKMYT1 protein kinase, membrane associated tyrosine/threonine 1
PLK4 polo-like kinase 4
POLA2 polymerase (DNA directed), alpha 2 (70kD subunit)
POLD1 polymerase (DNA directed), delta 1, catalytic subunit 125kDa
POLE2 polymerase (DNA directed), epsilon 2 (p59 subunit)
POLR2D polymerase (RNA) II (DNA directed) polypeptide D
POLR2K polymerase (RNA) II (DNA directed) polypeptide K, 7.0kDa
PPP1CC protein phosphatase 1, catalytic subunit, gamma isozyme
PRC1 protein regulator of cytokinesis 1
PRKDC protein kinase, DNA-activated, catalytic polypeptide
PSEN2 presenilin 2 (Alzheimer disease 4)
PSMA1 proteasome (prosome, macropain) subunit, alpha type, 1
PSMA6 proteasome (prosome, macropain) subunit, alpha type, 6
PSMB3 proteasome (prosome, macropain) subunit, beta type, 3
PSMB4 proteasome (prosome, macropain) subunit, beta type, 4
PSMB5 proteasome (prosome, macropain) subunit, beta type, 5
PSMC1 proteasome (prosome, macropain) 26S subunit, ATPase, 1
PSMC4 proteasome (prosome, macropain) 26S subunit, ATPase, 4
PSMC5 proteasome (prosome, macropain) 26S subunit, ATPase, 5
PSMC6 proteasome (prosome, macropain) 26S subunit, ATPase, 6
PSMD1 proteasome (prosome, macropain) 26S subunit, non-ATPase, 1
PSMD11 proteasome (prosome, macropain) 26S subunit, non-ATPase, 11
PSMD14 proteasome (prosome, macropain) 26S subunit, non-ATPase, 14
PSMD2 proteasome (prosome, macropain) 26S subunit, non-ATPase, 2
PSMD6 proteasome (prosome, macropain) 26S subunit, non-ATPase, 6
PSMD8 proteasome (prosome, macropain) 26S subunit, non-ATPase, 8
PSME3 proteasome (prosome, macropain) activator subunit 3 (PA28 gamma; Ki)
PSPH phosphoserine phosphatase
PTDSS1 phosphatidylserine synthase 1
PTK2 PTK2 protein tyrosine kinase 2
PTPN12 protein tyrosine phosphatase, non-receptor type 12
PTPRF protein tyrosine phosphatase, receptor type, F
PTTG1 pituitary tumor-transforming 1
PYCR2 pyrroline-5-carboxylate reductase family, member 2
PYGB phosphorylase, glycogen; brain
RABGGTB Rab geranylgeranyltransferase, beta subunit
RACGAP1 Rac GTPase activating protein 1
RAD21 RAD21 homolog (S. pombe)
RAN RAN, member RAS oncogene family
RARS arginyl-tRNA synthetase
RBBP4 retinoblastoma binding protein 4
RBBP7 retinoblastoma binding protein 7
RBL1 retinoblastoma-like 1 (p107)
RBM17 RNA binding motif protein 17
RBM3 RNA binding motif (RNP1, RRM) protein 3
RCN2 reticulocalbin 2, EF-hand calcium binding domain
RFC3 replication factor C (activator 1) 3, 38kDa
RFC4 replication factor C (activator 1) 4, 37kDa
RFC5 replication factor C (activator 1) 5, 36.5kDa
RNF4 ring finger protein 4
RPA3 replication protein A3, 14kDa
RRAGD Ras-related GTP binding D
RRM1 ribonucleotide reductase M1
RRM2 ribonucleotide reductase M2
SCARB2 scavenger receptor class B, member 2
SGOL2 shugoshin-like 2 (S. pombe)
SLBP stem-loop binding protein
SLC1A4 solute carrier family 1 (glutamate/neutral amino acid transporter), member 4
SLC25A6 solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 6
SLC29A1 solute carrier family 29 (nucleoside transporters), member 1
SLC35B1 solute carrier family 35, member B1
SLC39A6 solute carrier family 39 (zinc transporter), member 6
SMAD3 SMAD family member 3
SMARCC1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1
SMC3 structural maintenance of chromosomes 3
SMC4 structural maintenance of chromosomes 4
SMS spermine synthase
SNRPD3 small nuclear ribonucleoprotein D3 polypeptide 18kDa
SNRPE small nuclear ribonucleoprotein polypeptide E
SNRPF small nuclear ribonucleoprotein polypeptide F
SNRPG small nuclear ribonucleoprotein polypeptide G
SNX12 sorting nexin 12
SOX4 SRY (sex determining region Y)-box 4
SP3 Sp3 transcription factor
SPINK1 serine peptidase inhibitor, Kazal type 1
SQLE squalene epoxidase
SRPK1 SRSF protein kinase 1
SSB Sjogren syndrome antigen B (autoantigen La)
SSBP1 single-stranded DNA binding protein 1
SSR2 signal sequence receptor, beta (translocon-associated protein beta)
SSRP1 structure specific recognition protein 1
STMN1 stathmin 1
STRAP serine/threonine kinase receptor associated protein
SYPL1 synaptophysin-like 1
TAF9 TAF9 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 32kDa
TARBP1 TAR (HIV-1) RNA binding protein 1
TARS threonyl-tRNA synthetase
TCEA1 transcription elongation factor A (SII), 1
TCF12 transcription factor 12
TDP2 tyrosyl-DNA phosphodiesterase 2
TIMM17A translocase of inner mitochondrial membrane 17 homolog A (yeast)
TIMM50 translocase of inner mitochondrial membrane 50 homolog (S. cerevisiae)
TMCO1 transmembrane and coiled-coil domains 1
TMEM106C transmembrane protein 106C
TMEM97 transmembrane protein 97
TMPO thymopoietin
TOMM20 translocase of outer mitochondrial membrane 20 homolog (yeast)
TOP2A topoisomerase (DNA) II alpha 170kDa
TOPBP1 topoisomerase (DNA) II binding protein 1
TP53BP2 tumor protein p53 binding protein, 2
TPX2 TPX2, microtubule-associated, homolog (Xenopus laevis)
TRAM1 translocation associated membrane protein 1
TRIM24 tripartite motif containing 24
TRIP13 thyroid hormone receptor interactor 13
TTK TTK protein kinase
TXN thioredoxin
TXNL1 thioredoxin-like 1
TXNRD1 thioredoxin reductase 1
TYMS thymidylate synthetase
UBE2A ubiquitin-conjugating enzyme E2A (RAD6 homolog)
UBE2C ubiquitin-conjugating enzyme E2C
UBE2D2 ubiquitin-conjugating enzyme E2D 2 (UBC4/5 homolog, yeast)
UBE2T ubiquitin-conjugating enzyme E2T (putative)
UCHL5 ubiquitin carboxyl-terminal hydrolase L5
UCK2 uridine-cytidine kinase 2
USP1 ubiquitin specific peptidase 1
VBP1 von Hippel-Lindau binding protein 1
VDAC1 voltage-dependent anion channel 1
VPS13B vacuolar protein sorting 13 homolog B (yeast)
VPS72 vacuolar protein sorting 72 homolog (S. cerevisiae)
WDHD1 WD repeat and HMG-box DNA binding protein 1
WDR45L WDR45-like
WHSC1 Wolf-Hirschhorn syndrome candidate 1
XPO1 exportin 1 (CRM1 homolog, yeast)
XPOT exportin, tRNA (nuclear export receptor for tRNAs)
YWHAG tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma polypeptide
YWHAH tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide
YWHAZ tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide
ZIC2 Zic family member 2 (odd-paired homolog, Drosophila)
ZWILCH Zwilch, kinetochore associated, homolog (Drosophila)
ZWINT ZW10 interactor

The following is the Master Liver Gene List from our analysis.

Symbol Entrez Gene Name
A2M alpha-2-macroglobulin
AASS aminoadipate-semialdehyde synthase
ABCA8 ATP-binding cassette, sub-family A (ABC1), member 8
ABCB4 ATP-binding cassette, sub-family B (MDR/TAP), member 4
ABCC2 ATP-binding cassette, sub-family C (CFTR/MRP), member 2
ABHD2 abhydrolase domain containing 2
ABL1 c-abl oncogene 1, non-receptor tyrosine kinase
ABLIM3 actin binding LIM protein family, member 3
ACAA1 acetyl-CoA acyltransferase 1
ACAA2 acetyl-CoA acyltransferase 2
ACADL acyl-CoA dehydrogenase, long chain
ACADS acyl-CoA dehydrogenase, C-2 to C-3 short chain
ACADSB acyl-CoA dehydrogenase, short/branched chain
ACO1 aconitase 1, soluble
ACOX1 acyl-CoA oxidase 1, palmitoyl
ACOX2 acyl-CoA oxidase 2, branched chain
ACSL1 acyl-CoA synthetase long-chain family member 1
ACSM3 acyl-CoA synthetase medium-chain family member 3
ACVR2A activin A receptor, type IIA
ACY1 aminoacylase 1
ADAMDEC1 ADAM-like, decysin 1
ADAMTS2 ADAM metallopeptidase with thrombospondin type 1 motif, 2
ADCY5 adenylate cyclase 5
ADH1B alcohol dehydrogenase 1B (class I), beta polypeptide
ADH1C alcohol dehydrogenase 1C (class I), gamma polypeptide
ADH4 alcohol dehydrogenase 4 (class II), pi polypeptide
ADH5 alcohol dehydrogenase 5 (class III), chi polypeptide
ADH6 alcohol dehydrogenase 6 (class V)
ADHFE1 alcohol dehydrogenase, iron containing, 1
AEBP1 AE binding protein 1
AGL amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase
AGXT alanine-glyoxylate aminotransferase
AKAP13 A kinase (PRKA) anchor protein 13
AKAP7 A kinase (PRKA) anchor protein 7
ALAS1 aminolevulinate, delta-, synthase 1
ALAS2 aminolevulinate, delta-, synthase 2
ALB albumin
ALDH2 aldehyde dehydrogenase 2 family (mitochondrial)
ALDH6A1 aldehyde dehydrogenase 6 family, member A1
ALDH9A1 aldehyde dehydrogenase 9 family, member A1
ALDOB aldolase B, fructose-bisphosphate
ALOX5 arachidonate 5-lipoxygenase
AOC3 amine oxidase, copper containing 3 (vascular adhesion protein 1)
APOA1 apolipoprotein A-I
APOB apolipoprotein B (including Ag(x) antigen)
APOC4 apolipoprotein C-IV
APOH apolipoprotein H (beta-2-glycoprotein I)
AQP3 aquaporin 3 (Gill blood group)
AQP9 aquaporin 9
AR androgen receptor
ARG1 arginase, liver
ASGR1 asialoglycoprotein receptor 1
ASGR2 asialoglycoprotein receptor 2
ASPA aspartoacylase
ASS1 argininosuccinate synthase 1
ATP1A2 ATPase, Na+/K+ transporting, alpha 2 polypeptide
ATP2B1 ATPase, Ca++ transporting, plasma membrane 1
AXL AXL receptor tyrosine kinase
AZGP1 alpha-2-glycoprotein 1, zinc-binding
BASP1 brain abundant, membrane attached signal protein 1
BBOX1 butyrobetaine (gamma), 2-oxoglutarate dioxygenase (gamma-butyrobetaine hydroxylase) 1
BCKDHB branched chain keto acid dehydrogenase E1, beta polypeptide
BDH1 3-hydroxybutyrate dehydrogenase, type 1
BMP6 bone morphogenetic protein 6
C1R complement component 1, r subcomponent
C1S complement component 1, s subcomponent
C6 complement component 6
C7 complement component 7
C8A complement component 8, alpha polypeptide
C8B complement component 8, beta polypeptide
C8orf4 chromosome 8 open reading frame 4
CA2 carbonic anhydrase II
CALM1 (includes others) calmodulin 1 (phosphorylase kinase, delta)
CAT catalase
CBR4 carbonyl reductase 4
CBS cystathionine-beta-synthase
CCL2 chemokine (C-C motif) ligand 2
CCL3 chemokine (C-C motif) ligand 3
CCND1 cyclin D1
CCR1 chemokine (C-C motif) receptor 1
CD14 CD14 molecule
CD2 CD2 molecule
CD302 CD302 molecule
CD53 CD53 molecule
CD5L CD5 molecule-like
CD69 CD69 molecule
CD79A CD79a molecule, immunoglobulin-associated alpha
CD83 CD83 molecule
CD9 CD9 molecule
CDH15 cadherin 15, type 1, M-cadherin (myotubule)
CDO1 cysteine dioxygenase, type I
CEBPD CCAAT/enhancer binding protein (C/EBP), delta
CELF2 CUGBP, Elav-like family member 2
CFB complement factor B
CFD complement factor D (adipsin)
CFP complement factor properdin
CHI3L2 chitinase 3-like 2
CLDN10 claudin 10
COL14A1 collagen, type XIV, alpha 1
COLEC10 collectin sub-family member 10 (C-type lectin)
CPB2 carboxypeptidase B2 (plasma)
CPT2 carnitine palmitoyltransferase 2
CR1 complement component (3b/4b) receptor 1 (Knops blood group)
CRADD CASP2 and RIPK1 domain containing adaptor with death domain
CRHBP corticotropin releasing hormone binding protein
CRISPLD2 cysteine-rich secretory protein LCCL domain containing 2
CSF1R colony stimulating factor 1 receptor
CSPG5 chondroitin sulfate proteoglycan 5 (neuroglycan C)
CTAGE5 CTAGE family, member 5
CTSW cathepsin W
CXCL1 chemokine (C-X-C motif) ligand 1 (melanoma growth stimulating activity, alpha)
CXCL12 chemokine (C-X-C motif) ligand 12
CXCL14 chemokine (C-X-C motif) ligand 14
CXCL2 chemokine (C-X-C motif) ligand 2
CXCL3 chemokine (C-X-C motif) ligand 3
CYB5A cytochrome b5 type A (microsomal)
CYBB cytochrome b-245, beta polypeptide
CYP17A1 cytochrome P450, family 17, subfamily A, polypeptide 1
CYP1A1 cytochrome P450, family 1, subfamily A, polypeptide 1
CYP26A1 cytochrome P450, family 26, subfamily A, polypeptide 1
CYP2A6 (includes others) cytochrome P450, family 2, subfamily A, polypeptide 6
CYP2B6 cytochrome P450, family 2, subfamily B, polypeptide 6
CYP2C18 cytochrome P450, family 2, subfamily C, polypeptide 18
CYP2C8 cytochrome P450, family 2, subfamily C, polypeptide 8
CYP2C9 cytochrome P450, family 2, subfamily C, polypeptide 9
CYP2E1 cytochrome P450, family 2, subfamily E, polypeptide 1
CYP2J2 cytochrome P450, family 2, subfamily J, polypeptide 2
CYP3A5 cytochrome P450, family 3, subfamily A, polypeptide 5
CYP3A7 cytochrome P450, family 3, subfamily A, polypeptide 7
CYP4A11 cytochrome P450, family 4, subfamily A, polypeptide 11
CYP4F12 cytochrome P450, family 4, subfamily F, polypeptide 12
DAPK1 death-associated protein kinase 1
DCN decorin
DCT dopachrome tautomerase (dopachrome delta-isomerase, tyrosine-related protein 2)
DCXR dicarbonyl/L-xylulose reductase
DLG4 discs, large homolog 4 (Drosophila)
DMD dystrophin
DNASE1L3 deoxyribonuclease I-like 3
DPP4 dipeptidyl-peptidase 4
DPT dermatopontin
DPYS dihydropyrimidinase
DSG1 desmoglein 1
DTNB dystrobrevin, beta
ECHDC2 enoyl CoA hydratase domain containing 2
ECHS1 enoyl CoA hydratase, short chain, 1, mitochondrial
EDNRB endothelin receptor type B
EGR1 early growth response 1
EIF2B2 eukaryotic translation initiation factor 2B, subunit 2 beta, 39kDa
EPB41L3 erythrocyte membrane protein band 4.1-like 3
EPHX2 epoxide hydrolase 2, cytoplasmic
ERCC4 excision repair cross-complementing rodent repair deficiency, complementation group 4
ERG v-ets erythroblastosis virus E26 oncogene homolog (avian)
ETV6 ets variant 6
EVL Enah/Vasp-like
F11 coagulation factor XI
F2 coagulation factor II (thrombin)
FAAH fatty acid amide hydrolase
FAH fumarylacetoacetate hydrolase (fumarylacetoacetase)
FAM46C family with sequence similarity 46, member C
FBLN5 fibulin 5
FBP1 fructose-1,6-bisphosphatase 1
FBXO21 F-box protein 21
FCN2 ficolin (collagen/fibrinogen domain containing lectin) 2 (hucolin)
FEZ1 fasciculation and elongation protein zeta 1 (zygin I)
FGF2 fibroblast growth factor 2 (basic)
FGG fibrinogen gamma chain
FGR Gardner-Rasheed feline sarcoma viral (v-fgr) oncogene homolog
FLT4 fms-related tyrosine kinase 4
FMO2 flavin containing monooxygenase 2 (non-functional)
FOLH1 folate hydrolase (prostate-specific membrane antigen) 1
FOS FBJ murine osteosarcoma viral oncogene homolog
FOSB FBJ murine osteosarcoma viral oncogene homolog B
FOXO1 forkhead box O1
FPR1 formyl peptide receptor 1
FRK fyn-related kinase
FYN FYN oncogene related to SRC, FGR, YES
GABARAPL1 GABA(A) receptor-associated protein like 1
GCDH glutaryl-CoA dehydrogenase
GCH1 GTP cyclohydrolase 1
GHR growth hormone receptor
GLDC glycine dehydrogenase (decarboxylating)
GLT8D2 glycosyltransferase 8 domain containing 2
GLYAT glycine-N-acyltransferase
GNA14 guanine nucleotide binding protein (G protein), alpha 14
GNAO1 guanine nucleotide binding protein (G protein), alpha activating activity polypeptide O
GNG2 guanine nucleotide binding protein (G protein), gamma 2
GPD1 glycerol-3-phosphate dehydrogenase 1 (soluble)
GPM6A glycoprotein M6A
GPR18 G protein-coupled receptor 18
GRAMD1C GRAM domain containing 1C
GSTA3 glutathione S-transferase alpha 3
GSTZ1 glutathione transferase zeta 1
GYS2 glycogen synthase 2 (liver)
H2AFV H2A histone family, member V
HAAO 3-hydroxyanthranilate 3,4-dioxygenase
HAL histidine ammonia-lyase
HAMP hepcidin antimicrobial peptide
HAO1 hydroxyacid oxidase (glycolate oxidase) 1
HBD hemoglobin, delta
HCK hemopoietic cell kinase
HGF hepatocyte growth factor (hepapoietin A; scatter factor)
HIBCH 3-hydroxyisobutyryl-CoA hydrolase
HMGCL 3-hydroxymethyl-3-methylglutaryl-CoA lyase
HMGCS2 3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial)
HP haptoglobin
HPD 4-hydroxyphenylpyruvate dioxygenase
HPX hemopexin
HRG histidine-rich glycoprotein
HSD11B1 hydroxysteroid (11-beta) dehydrogenase 1
ID1 inhibitor of DNA binding 1, dominant negative helix-loop-helix protein
ID2 inhibitor of DNA binding 2, dominant negative helix-loop-helix protein
ID2B inhibitor of DNA binding 2B, dominant negative helix-loop-helix protein (pseudogene)
IFI44L interferon-induced protein 44-like
IFITM1 interferon induced transmembrane protein 1 (9-27)
IFNAR1 interferon (alpha, beta and omega) receptor 1
IGF1 insulin-like growth factor 1 (somatomedin C)
IGF2 insulin-like growth factor 2 (somatomedin A)
IGFBP1 insulin-like growth factor binding protein 1
IGFBP3 insulin-like growth factor binding protein 3
IGHD immunoglobulin heavy constant delta
IL12RB1 interleukin 12 receptor, beta 1
IL1B interleukin 1, beta
IL1RAP interleukin 1 receptor accessory protein
IL2RB interleukin 2 receptor, beta
IL4R interleukin 4 receptor
IL6ST interleukin 6 signal transducer (gp130, oncostatin M receptor)
INPP5E inositol polyphosphate-5-phosphatase, 72 kDa
IQGAP1 IQ motif containing GTPase activating protein 1
IRF8 interferon regulatory factor 8
ITGA2 integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)
ITGA9 integrin, alpha 9
ITGAL integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)
ITIH4 inter-alpha (globulin) inhibitor H4 (plasma Kallikrein-sensitive glycoprotein)
ITIH5 inter-alpha (globulin) inhibitor H5
JAG2 jagged 2
JUN jun proto-oncogene
KAL1 Kallmann syndrome 1 sequence
KBTBD11 kelch repeat and BTB (POZ) domain containing 11
KCNMA1 potassium large conductance calcium-activated channel, subfamily M, alpha member 1
KHK ketohexokinase (fructokinase)
KLF9 Kruppel-like factor 9
KLKB1 kallikrein B, plasma (Fletcher factor) 1
KMO kynurenine 3-monooxygenase (kynurenine 3-hydroxylase)
KRT7 keratin 7
KYNU kynureninase
LAMC2 laminin, gamma 2
LARP4 La ribonucleoprotein domain family, member 4
LCAT lecithin-cholesterol acyltransferase
LGMN legumain
LIFR leukemia inhibitory factor receptor alpha
LIPC lipase, hepatic
LMO7 LIM domain 7
LPA lipoprotein, Lp(a)
LST1 leukocyte specific transcript 1
LTK leukocyte receptor tyrosine kinase
LY75 lymphocyte antigen 75
MAN1C1 mannosidase, alpha, class 1C, member 1
MARCO macrophage receptor with collagenous structure
MASP2 mannan-binding lectin serine peptidase 2
MBL2 mannose-binding lectin (protein C) 2, soluble
MBNL2 muscleblind-like 2 (Drosophila)
MCC mutated in colorectal cancers
MEF2A myocyte enhancer factor 2A
METTL7A methyltransferase like 7A
MFAP3L microfibrillar-associated protein 3-like
MFAP4 microfibrillar-associated protein 4
MGST2 microsomal glutathione S-transferase 2
MME membrane metallo-endopeptidase
MMP14 matrix metallopeptidase 14 (membrane-inserted)
MRC2 mannose receptor, C type 2
MRPL46 mitochondrial ribosomal protein L46
MS4A6A membrane-spanning 4-domains, subfamily A, member 6A
MST1 macrophage stimulating 1 (hepatocyte growth factor-like)
MT-TP tRNA
MT1B metallothionein 1B
MT1E metallothionein 1E
MT1H metallothionein 1H
MT1X metallothionein 1X
MTHFD1 methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase
MUSK muscle, skeletal, receptor tyrosine kinase
MXRA5 matrix-remodelling associated 5
MYBPC2 myosin binding protein C, fast type
MYD88 myeloid differentiation primary response gene (88)
MYH10 myosin, heavy chain 10, non-muscle
MYO10 myosin X
NAT1 N-acetyltransferase 1 (arylamine N-acetyltransferase)
NAT2 N-acetyltransferase 2 (arylamine N-acetyltransferase)
NELL2 NEL-like 2 (chicken)
NFIL3 nuclear factor, interleukin 3 regulated
NKG7 natural killer cell group 7 sequence
NNMT nicotinamide N-methyltransferase
NPY1R neuropeptide Y receptor Y1
NR3C2 nuclear receptor subfamily 3, group C, member 2
NR4A1 nuclear receptor subfamily 4, group A, member 1
NRP2 neuropilin 2
NRXN2 neurexin 2
NTRK2 neurotrophic tyrosine kinase, receptor, type 2
OLFM1 olfactomedin 1
OLFML1 olfactomedin-like 1
OLFML3 olfactomedin-like 3
ORM1/ORM2 orosomucoid 1
ORM1/ORM2 orosomucoid 1
OSBPL5 oxysterol binding protein-like 5
PAPPA pregnancy-associated plasma protein A, pappalysin 1
PCBD1 pterin-4 alpha-carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha
PCK1 phosphoenolpyruvate carboxykinase 1 (soluble)
PCK2 phosphoenolpyruvate carboxykinase 2 (mitochondrial)
PCOLCE procollagen C-endopeptidase enhancer
PDE1A phosphodiesterase 1A, calmodulin-dependent
PDE1C phosphodiesterase 1C, calmodulin-dependent 70kDa
PDE4D phosphodiesterase 4D, cAMP-specific
PDE4DIP phosphodiesterase 4D interacting protein
PDE7B phosphodiesterase 7B
PDGFRA platelet-derived growth factor receptor, alpha polypeptide
PDLIM5 PDZ and LIM domain 5
PEBP1 phosphatidylethanolamine binding protein 1
PHLDA1 pleckstrin homology-like domain, family A, member 1
PHYH phytanoyl-CoA 2-hydroxylase
PLA2G4A phospholipase A2, group IVA (cytosolic, calcium-dependent)
PLAC8 placenta-specific 8
PLAU plasminogen activator, urokinase
PLCB2 phospholipase C, beta 2
PLD3 phospholipase D family, member 3
PLEK pleckstrin
PLG plasminogen
PLIN2 perilipin 2
PLP1 proteolipid protein 1
PLTP phospholipid transfer protein
PON1 paraoxonase 1
PON3 paraoxonase 3
PPAP2B phosphatidic acid phosphatase type 2B
PPP1R13B protein phosphatase 1, regulatory (inhibitor) subunit 13B
PRELP proline/arginine-rich end leucine-rich repeat protein
PRKAA1 protein kinase, AMP-activated, alpha 1 catalytic subunit
PRKCH protein kinase C, eta
PRKCQ protein kinase C, theta
PRKG1 protein kinase, cGMP-dependent, type I
PRRX1 paired related homeobox 1
PRTN3 proteinase 3
PTGIS prostaglandin I2 (prostacyclin) synthase
PTGR1 prostaglandin reductase 1
PTGS1 prostaglandin-endoperoxide synthase 1 (prostaglandin G/H synthase and cyclooxygenase)
PTGS2 prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)
PTH1R parathyroid hormone 1 receptor
PTPN13 protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)
PTPRC protein tyrosine phosphatase, receptor type, C
PYGL phosphorylase, glycogen, liver
PZP pregnancy-zone protein
QDPR quinoid dihydropteridine reductase
RAPGEF2 Rap guanine nucleotide exchange factor (GEF) 2
RASGEF1B RasGEF domain family, member 1B
RBP4 retinol binding protein 4, plasma
RBP5 retinol binding protein 5, cellular
RCAN1 regulator of calcineurin 1
RCOR1 REST corepressor 1
RELN reelin
RGN regucalcin (senescence marker protein-30)
RHOB ras homolog gene family, member B
RNASE4 ribonuclease, RNase A family, 4
RXRG retinoid X receptor, gamma
SAA4 serum amyloid A4, constitutive
SC5DL sterol-C5-desaturase (ERG3 delta-5-desaturase homolog, S. cerevisiae)-like
SCAF11 SR-related CTD-associated factor 11
SCARF1 scavenger receptor class F, member 1
SELE selectin E
SELP selectin P (granule membrane protein 140kDa, antigen CD62)
SEMA3C sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C
SERPINA1 serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1
SERPING1 serpin peptidase inhibitor, clade G (C1 inhibitor), member 1
SHMT2 serine hydroxymethyltransferase 2 (mitochondrial)
SKAP1 src kinase associated phosphoprotein 1
SLC10A1 solute carrier family 10 (sodium/bile acid cotransporter family), member 1
SLC17A3 solute carrier family 17 (sodium phosphate), member 3
SLC17A7 solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 7
SLC1A1 solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1
SLC1A2 solute carrier family 1 (glial high affinity glutamate transporter), member 2
SLC22A1 solute carrier family 22 (organic cation transporter), member 1
SLC27A5 solute carrier family 27 (fatty acid transporter), member 5
SLC41A1 solute carrier family 41, member 1
SLC4A4 solute carrier family 4, sodium bicarbonate cotransporter, member 4
SLC6A8 solute carrier family 6 (neurotransmitter transporter, creatine), member 8
SMAD6 SMAD family member 6
SMARCA2 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2
SOCS3 suppressor of cytokine signaling 3
SOD1 superoxide dismutase 1, soluble
SORL1 sortilin-related receptor, L(DLR class) A repeats containing
SOX17 SRY (sex determining region Y)-box 17
SPIB Spi-B transcription factor (Spi-1/PU.1 related)
SPON1 spondin 1, extracellular matrix protein
SPP2 secreted phosphoprotein 2, 24kDa
SRD5A2 steroid-5-alpha-reductase, alpha polypeptide 2 (3-oxo-5 alpha-steroid delta 4-dehydrogenase alpha 2)
SRPX sushi-repeat containing protein, X-linked
ST3GAL6 ST3 beta-galactoside alpha-2,3-sialyltransferase 6
ST8SIA4 ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4
STAB1 stabilin 1
SULT4A1 sulfotransferase family 4A, member 1
TACSTD2 tumor-associated calcium signal transducer 2
TBXA2R thromboxane A2 receptor
TBXAS1 thromboxane A synthase 1 (platelet)
TCN1 transcobalamin I (vitamin B12 binding protein, R binder family)
TDO2 tryptophan 2,3-dioxygenase
TEK TEK tyrosine kinase, endothelial
TF transferrin
TFAP2A transcription factor AP-2 alpha (activating enhancer binding protein 2 alpha)
TGFB1I1 transforming growth factor beta 1 induced transcript 1
TGFBR2 transforming growth factor, beta receptor II (70/80kDa)
TGFBR3 transforming growth factor, beta receptor III
TGM2 transglutaminase 2 (C polypeptide, protein-glutamine-gamma-glutamyltransferase)
THBS1 thrombospondin 1
TIAM1 T-cell lymphoma invasion and metastasis 1
TNFRSF1A tumor necrosis factor receptor superfamily, member 1A
TNXB tenascin XB
TPSAB1/TPSB2 tryptase alpha/beta 1
TRAM2 translocation associated membrane protein 2
UAP1 UDP-N-acteylglucosamine pyrophosphorylase 1
UCP2 uncoupling protein 2 (mitochondrial, proton carrier)
UGT2B15 UDP glucuronosyltransferase 2 family, polypeptide B15
UGT2B4 UDP glucuronosyltransferase 2 family, polypeptide B4
UGT2B7 UDP glucuronosyltransferase 2 family, polypeptide B7
ULK2 unc-51-like kinase 2 (C. elegans)
VAV1 vav 1 guanine nucleotide exchange factor
VIPR1 vasoactive intestinal peptide receptor 1
VNN1 vanin 1
VSIG4 V-set and immunoglobulin domain containing 4
WNT11 wingless-type MMTV integration site family, member 11
WNT2 wingless-type MMTV integration site family member 2
YES1 v-yes-1 Yamaguchi sarcoma viral oncogene homolog 1
ZAP70 zeta-chain (TCR) associated protein kinase 70kDa
ZG16 zymogen granule protein 16 homolog (rat)
ZNF185 zinc finger protein 185 (LIM domain)
ZNF238 zinc finger protein 238

The following 7 Gene Sets had highly significant enrichment scores for uninvolved liver genes adjacent to HCCs. All Gene Sets are from the msigdb_v2.5.xml database from the Gene Set Enrichment Analysis software available from the Broad Institute (http://www.broadinstitute.org/gsea/index.jsp).

1. FETAL_LIVER_VS_ADULT_LIVER_GNF2

Genes upregulated in fetal liver vs adult liver

Contributed to GSEA by Jean-Pierre Bourquin

ABCC3 ATP-binding cassette, sub-family C (CFTR/MRP), member 3
ABHD2 abhydrolase domain containing 2
ACY1 aminoacylase 1
ADH1C alcohol dehydrogenase 1C (class I), gamma polypeptide
APCS amyloid P component, serum
APOC4 apolipoprotein C-IV
AQP9 aquaporin 9
ASL argininosuccinate lyase
AZGP1 alpha-2-glycoprotein 1, zinc
C1R complement component 1, r subcomponent
C6orf108 chromosome 6 open reading frame 108
C8G complement component 8, gamma polypeptide
CD14 CD14 molecule
CD151 CD151 molecule (Raph blood group)
CD81 CD81 molecule
CES1 carboxylesterase 1 (monocyte/macrophage serine esterase 1)
CES2 carboxylesterase 2 (intestine, liver)
CLPP ClpP caseinolytic peptidase, ATP-dependent, proteolytic subunit homolog (E. coli)
COMT catechol-O-methyltransferase
CYP1A2 cytochrome P450, family 1, subfamily A, polypeptide 2
CYP27A1 cytochrome P450, family 27, subfamily A, polypeptide 1
CYP2A6 cytochrome P450, family 2, subfamily A, polypeptide 6
CYP2B6 cytochrome P450, family 2, subfamily B, polypeptide 6
CYP2C8 cytochrome P450, family 2, subfamily C, polypeptide 8
CYP2C9 cytochrome P450, family 2, subfamily C, polypeptide 9
CYP2E1 cytochrome P450, family 2, subfamily E, polypeptide 1
CYP4A11 cytochrome P450, family 4, subfamily A, polypeptide 11
DCPS decapping enzyme, scavenger
DEXI -
DKFZp451J0118

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