Table 2 Summary of selected genes

From: Application of comparative functional genomics to identify best-fit mouse models to study human cancer

Unigene Gene symbol   Log ratio (A/B) *
Human Mouse Human Mouse Description Human Mouse
Nuclear pore transport
Hs.113503 Mm.151329 RANBP5 Kpnb3 Karyopherin (importin) beta 3 0.97 0.81
Hs.180446 Mm.16710 KPNB1 Kpnb1 Karyopherin (importin) beta 1 0.98 0.75
Hs.90073 Mm.22417 CSE1L Cse1l Chromosome segregation 1-like (budding yeast); Exportin 1.13 0.90
Anti-apoptosis
Hs.75462 Mm.239605 BTG2 Btg2 BTG family, member 2 0.71 1.46
Hs.171391 Mm.226905 CTBP2 Ctbp2 C-terminal binding protein 2 0.80 0.75
Hs.75562 Mm.5021 DDR1 Ddr1 Discoidin domain receptor family, member 1 0.69 1.49
Hs.180414 Mm.197551 HSPA8 Hspa8 Heat shock 70kDa protein 8 0.77 1.25
Hs.145279 Mm.28805 SET Set SET translocation (myeloid leukemia-associated) 1.03 0.76
Hs.115770 Mm.6426 TNFSF11 Tnfsf11 Tumor necrosis factor (ligand) superfamily, member 11 0.81 0.85
Hs.373508 Mm.3399 TRAF2 Traf2 TNF receptor-associated factor 2 0.67 0.78
Hs.349530 Mm.3308 YWHAH Ywhah Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein 1.12 0.88
Cell growth and proliferation
Hs.152759 Mm.22430 ASK Ask Activator of S phase kinase 1.15 0.96
Hs.1634 Mm.29800 CDC25A Cdc25a Cell division cycle 25A 0.58 1.32
Hs.28853 Mm.20842 CDC7 Cdc7 CDC7 Cell division cycle 7-like 1 (budding yeast) 0.84 0.95
Hs.95577 Mm.6839 CDK4 Cdk4 Cyclin-dependent kinase 4 1.31 0.93
Hs.122579 Mm.2995 ECT2 Ect2 Epithelial cell transforming sequence 2 oncogene 1.39 0.98
Hs.401150 Mm.15918 MAP3K1 Map3k1 Mitogen-activated protein kinase kinase kinase 1 0.53 1.48
Hs.861 Mm.8385 MAPK3 Mapk3 Mitogen-activated protein kinase 3 0.85 0.81
Hs.179565 Mm.4502 MCM3 Mcm3 Minichromosome maintenance deficient 3 1.09 1.02
Hs.155462 Mm.4933 MCM6 Mcm6 Minichromosome maintenance deficient 6 1.25 1.34
Hs.89901 Mm.36865 PDE4A Pde4a Phosphodiesterase 4A 0.71 1.09
Hs.13501 Mm.28659 PES1 Pes1 Pescadillo homolog 1, containing BRCT domain (zebrafish) 0.93 0.78
Hs.93837 Mm.1860 PITPNM1 Pitpnm1 Phosphatidylinositol transfer protein, membrane-associated 1; Nir2 0.64 1.20
Hs.78944 Mm.28262 RGS2 Rgs2 Regulator of G-protein signaling 2, 24kDa 1.11 0.80
Hs.68061 Mm.20944 SPHK1 Sphk1 Sphingosine kinase 1 1.30 1.04
Hs.79150 Mm.46781 CCT4 Cct4 Chaperonin containing TCP1, subunit 4 (delta) 1.07 0.68
Hs.1600 Mm.1813 CCT5 Cct5 Chaperonin containing TCP1, subunit 5 (epsilon) 0.96 1.16
Hs.108809 Mm.914 CCT7 Cct7 Chaperonin containing TCP1, subunit 7 (eta) 1.06 0.75
Hs.178551 Mm.30066 RPL8 Rpl8 Ribosomal protein L8 0.73 1.08
Hs.182825 Mm.16423 RPL35 Rpl35 Ribosomal protein L35 1.04 0.97
Hs.406682 Mm.3229 RPL26 Rpl26 Ribosomal protein L26 0.98 0.90
Hs.425293 Mm.2424 RPL10A Rpl10a Ribosomal protein L10a 0.93 0.84
Hs.298262 Mm.103634 RPS19 Rps19 Ribosomal protein S19 1.22 0.78
Hs.433411 Mm.11376 RPL36 Rpl36 Ribosomal protein L36 0.93 0.77
Hs.180450 Mm.16775 RPS24 Rps24 Ribosomal protein S24 1.03 0.77
Hs.301547 Mm.5281 RPS7 Rps7 Ribosomal protein S7 0.95 0.74
Hs.380843 Mm.1139 RPS6 Rps6 Ribosomal protein S6 1.09 0.71
Hs.153 Mm.37835 RPL7 Rpl7 Ribosomal protein L7 0.58 1.17
Proteinases
Hs.78056 Mm.930 CTSL Ctsl Cathepsin L 0.70 0.73
Hs.18069 Mm.17185 LGMN Lgmn Legumain 0.74 1.04
Hs.2256 Mm.4825 MMP7 Mmp7 Matrix metalloproteinase 7 (matrilysin, uterine) 0.69 1.71
Hs.151738 Mm.4406 MMP9 Mmp9 Matrix metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa) 0.83 1.24
Hs.1695 Mm.2055 MMP12 Mmp12 Matrix metalloproteinase 12 (macrophage elastase) 0.67 0.79
Poor Prognosis Markers
Hs.375108 Mm.6417 CD24 Cd24 CD24 antigen (small cell lung carcinoma cluster 4 antigen) 0.99 1.45
Hs.433996 Mm.4426 CD63 Cd63 CD63 antigen (melanoma 1 antigen) 0.84 1.62
Hs.275243 Mm.100144 S100A6 S100a6 S100 calcium binding protein A6 (calcyclin) 1.20 1.20
Hs.8036 Mm.260157 RAB3D Rab3d Member RAS oncogene family 0.91 1.53
Hs.155421 Mm.80 AFP Afp Alpha-fetoprotein 0.97 1.45
Hs.82961 Mm.4641 TFF3 Tff3 Trefoil factor 3 (intestinal) 0.55 1.57
  1. *Average gene expression ratios (log2-transformed) between subclass A and subclass B in human HCCs and between cluster 1 (human subclass A–like) and cluster 2 (human subclass B–like) in mouse HCCs.
  2. We did not include the genes downregulated in subclass A, because most of these genes are involved in the metabolic pathways of the liver, and downregulation of these genes merely reflects the more severe loss of liver function (complete list of genes is available in Supplementary Table 1 online).