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©2007 Baishideng Publishing Group Co.
World J Gastroenterol. Jun 28, 2007; 13(24): 3323-3332
Published online Jun 28, 2007. doi: 10.3748/wjg.v13.i24.3323
Published online Jun 28, 2007. doi: 10.3748/wjg.v13.i24.3323
Table 1 Primer and probe sequences used to validate the microarray analysis by quantitative RT-PCR
Genes | Primer sequences | Tm | Amplifiedproducts |
β-actin | FP: CCTGGCACCCAGCACAAT | 58°C | 221 bp |
RP: GCTGATCCACATCTGCTGGAA | 58°C | ||
Probe: ATCAAGATCATTGCTCCTCCTGAGCGC | 68°C | ||
jun | FP: TGCAAAGATGGAAACGACCTT | 58°C | 76 bp |
RP: GCCGTAGGCGCCACTCT | 59°C | ||
Probe: TACGACGATGCCCTCAACGCCTC | 68°C | ||
myc | FP: CCCCTAGTGCTGCATGAAGAG | 59°C | 95 bp |
RP: TCCACAGACACCACATCAATTTC | 58°C | ||
Probe: CACCAGCAGCGACTCTGAAGAAGAACA | 68°C | ||
tp53 | FP: ATGAGGCCTTGGAATTAAAGGAT | 58°C | 98 bp |
RP: CGTAGACTGGCCCTTCTTGGT | 59°C | ||
Probe: CAGGGCTCACTCCAGCTACCCGAA | 68°C |
Table 2 Expression abundance of 121 liver tumor-associated genes during liver regeneration
Name | Gene | Associated | Fold | Comparison | |
Abbr. | to | difference | LT. | RRL. | |
The same in gene expression trend | |||||
Cyclin A2 | *Ccna2 | 2 | 45.1 | ↑ | ↑ |
WEE1 homolog | Wee1 | 2 | 20.9 | ↑ | ↑ |
Cyclin E1 | Ccne1 | 2 | 18.5 | ↑ | ↑ |
Proliferating cell nuclear antigen | Pcna | 2 | 10.6 | ↑ | ↑ |
Smoothened homolog | Smo | 1,2 | 3 | ↑ | ↑ |
Protein NIMA-interacting 1 | Pin1 | 2 | 2.5 | ↑ | ↑ |
Cyclin-dependent kinase 4 | Cdk4 | 2 | 2.5 | ↑ | ↑ |
NIMA (never in mitosis gene a)-related kinase 6 | Nek6 | 2 | 2.3 | ↑ | ↑ |
Aryl-hydrocarbon receptor | Ahr | 1 | 2.2 | ↑ | ↑ |
Serpin peptidase inhibitor, clade E, member 1 | Serpine1 | 2 | 16.7 | ↑ | ↑ |
Heat shock 27 kDa protein 1 | Hspb1 | 2 | 11 | ↑ | ↑ |
Transforming growth factor, beta 1 | Tgfb1 | 2 | 4 | ↑ | ↑ |
Granulin | Grn | 2 | 2.3 | ↑ | ↑ |
Myeloid cell leukemia sequence 1 | Mcl1 | 2,3 | 4.3 | ↑ | ↑ |
WNT1 inducible signaling pathway protein 1 | Wisp1 | 2,3 | 14.9 | ↑ | ↑ |
Selectin E | Sele | 2 | 12.9 | ↑ | ↑ |
Metastasis associated 1 | Mta1 | 2 | 9.6 | ↑ | ↑ |
TIMP metallopeptidase inhibitor 1 | Timp1 | 2 | 8.6 | ↑ | ↑ |
Integrin, alpha V | Itgav | 2 | 5.2 | ↑ | ↑ |
Discs, large homolog 7 | Dlg7 | 2 | 4.3 | ↑ | ↑ |
Lectin, galactoside-binding, soluble, 1 | Lgals1 | 2 | 3.7 | ↑ | ↑ |
ADAM metallopeptidase domain 17 | Adam17 | 2 | 2.7 | ↑ | ↑ |
Integrin, beta 1 | Itgb1 | 2 | 2.6 | ↑ | ↑ |
Calponin 1, basic, smooth muscle | Cnn1 | 2 | 7 | ↑ | ↑ |
Macrophage migration inhibitory factor | Mif | 2 | 3.2 | ↑ | ↑ |
Collagen, type XVIII, alpha 1 | Col18a1 | 2 | 3.1 | ↑ | ↑ |
Connective tissue growth factor | *Ctgf | 2 | 13.9 | ↑ | ↑ |
Hexokinase 2 | Hk2 | 2 | 8.9 | ↑ | ↑ |
Chemokine (C-C motif) ligand 20 | Ccl20 | 2 | 8 | ↑ | ↑ |
v-jun sarcoma virus 17 oncogene homolog | *Jun | 2 | 6.9 | ↑ | ↑ |
Methyl-CpG binding domain protein 2 | Mbd2 | 2 | 3 | ↑ | ↑ |
TERF1 (TRF1)-interacting nuclear factor 2 | Tinf2 | 1 | 2.8 | ↑ | ↑ |
FMS-like tyrosine kinase 1 | *Flt1 | 2 | 2.3 | ↑ | ↑ |
Proteasome 26S subunit, non-ATPase, 10 | Psmd10 | 2 | 2 | ↑ | ↑ |
Phosphatase and tensin homolog | Pten | 1,2 | 0.5 | ↓ | ↓ |
Cold shock domain protein A | Csda | 1 | 0.5 | ↓ | ↓ |
cAMP responsive element binding protein 3-like 3 | Creb3l3 | 1 | 0.4 | ↓ | ↓ |
v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog | Kit | 2 | 0.4 | ↓ | ↓ |
Gap junction protein, beta 1, 32 kDa | Gjb1 | 1,2 | 0.2 | ↓ | ↓ |
Trefoil factor 1 | Tff1 | 3 | 0.1 | ↓ | ↓ |
Caspase 9, apoptosis-related cysteine peptidase | Casp9 | 2 | 0.5 | ↓ | ↓ |
Deleted in liver cancer 1 | Dlc1 | 1,2 | 0.5 | ↓ | ↓ |
B-cell CLL/lymphoma 2 | Bcl2 | 2 | 0.3 | ↓ | ↓ |
Inhibitor of DNA binding 1 | Id1 | 1,2 | 0.3 | ↓ | ↓ |
Protein tyrosine phosphatase, receptor type, H | Ptprh | 2 | 0.2 | ↓ | ↓ |
CD74 molecule, major histocompatibility complex, class II invariant chain | Cd74 | 2 | 0.4 | ↓ | ↓ |
Hepatocyte growth factor | *Hgf | 1,2 | 0.4 | ↓ | ↓ |
Mannose-binding lectin (protein C) 2, soluble | Mbl2 | 2 | 0.2 | ↓ | ↓ |
The contrary in gene expression trend | |||||
Myelocytomatosis oncogene | Myc | 1,2 | 19.7 | ↓ | ↑ |
Sprouty homolog 2 | Spry2 | 2 | 8.1 | ↓ | ↑ |
Growth arrest and DNA-damage-inducible, beta | Gadd45b | 2 | 55.7 | ↓ | ↑ |
Serine peptidase inhibitor, Kunitz type, 2 | Spint2 | 2 | 7.2 | ↓ | ↑ |
MAD homolog 4 | Smad4 | 1,2 | 3 | ↓ | ↑ |
Fibrinogen-like 1 | Fgl1 | 2 | 2.2 | ↓ | ↑ |
Caspase 8, apoptosis-related cysteine peptidase | Casp8 | 2 | 10.6 | ↓ | ↑ |
Interferon gamma | Ifng | 1,2 | 6.5 | ↓ | ↑ |
Tumor protein p53 | Tp53 | 1,2,3 | 2.9 | ↓ | ↑ |
Early growth response 1 | *Egr1 | 2 | 18.6 | ↓ | ↑ |
Transcription factor 1, hepatic | Tcf1 | 2 | 6.8 | ↓ | ↑ |
O-6-methylguanine-DNA methyltransferase | Mgmt | 2 | 4.3 | ↓ | ↑ |
Glutathione S-transferase theta 1 | Gstt1 | 2 | 3.2 | ↓ | ↑ |
Glutathione S-transferase M1 | Gstm1 | 2 | 2.2 | ↓ | ↑ |
Wingless-type MMTV integration site family, member 1 | Wnt1 | 2 | 0.5 | ↑ | ↓ |
SHC (Src homology 2 domain containing) | Shc1 | 2 | 0.5 | ↑ | ↓ |
Transforming protein 1 | |||||
Inhibitor of kappaB kinase beta | Ikbkb | 1,2 | 0.3 | ↑ | ↓ |
FK506 binding protein 4, 59 kDa | Fkbp4 | 2 | 0.3 | ↑ | ↓ |
Transcription factor 7-like 2 | Tcf7l2 | 2 | 0.2 | ↑ | ↓ |
v-erb-b2 erythroblastic leukemia viral oncogene | Erbb2 | 3 | 0.1 | ↑ | ↓ |
Homolog 2 | |||||
Heat shock 70kDa protein 1A | Hspa1a | 2 | 0.2 | ↑ | ↓ |
Heat shock 70kDa protein 5 | Hspa5 | 1,2 | 0.1 | ↑ | ↓ |
High mobility group AT-hook 1 | Hmga1 | 2 | 0.4 | ↑ | ↓ |
Ras homolog gene family, member C | Rhoc | 2 | 0.3 | ↑ | ↓ |
Cortactin | Cttn | 2 | 0.1 | ↑ | ↓ |
Serpin peptidase inhibitor, clade B, member 3 | Serpinb3 | 2 | 0.1 | ↑ | ↓ |
Ephrin-B1 | Efnb1 | 2 | 0.4 | ↑ | ↓ |
Coagulation factor II | F2 | 1,2 | 0.3 | ↑ | ↓ |
Trefoil factor 3 | Tff3 | 2 | 0.3 | ↑ | ↓ |
Forkhead box A2 | Foxa2 | 2 | 0.4 | ↑ | ↓ |
Glycogen synthase kinase 3 beta | Gsk3b | 1,2 | 0.4 | ↑ | ↓ |
ATP-binding cassette, sub-family B, member 1A | *Abcb1a | 1 | 0.2 | ↑ | ↓ |
Solute carrier family 2 , member 1 | *Slc2a1 | 2 | 0.2 | ↑ | ↓ |
Apolipoprotein E | *Apoe | 2 | 0.1 | ↑ | ↓ |
The comparable in gene expression trend | |||||
Lysosomal-associated protein transmembrane 4B | Laptm4b | 2 | 2.3,0.5 | ↑ | ↑↓ |
Met proto-oncogene | *Met | 1,2,3 | 2.3,0.4 | ↑ | ↑↓ |
Nuclear factor of kappa light polypeptide gene enhancer in B-cells 1 (p105) | Nfkb1 | 2 | 2.3,0.4 | ↑ | ↑↓ |
Acyl-CoA synthetase long-chain family member 4 | Acsl4 | 2 | 2.1,0.4 | ↑ | ↑↓ |
X-box binding protein 1 | Xbp1 | 1 | 4.3,0.3 | ↑ | ↑↓ |
Nerve growth factor, beta polypeptide | Ngfb | 2 | 3.7,0.5 | ↑ | ↑↓ |
Stearoyl-Coenzyme A desaturase 1 | Scd1 | 1,2 | 3.5,0.3 | ↑ | ↑↓ |
Telomerase reverse transcriptase | Tert | 1,2,3 | 5.3,0.3 | ↑ | ↑↓ |
Telomeric repeat binding factor (NIMA-interacting) 1 | Terf1 | 1 | 2.2,0.4 | ↑ | ↑↓ |
Cadherin 17 | Cdh17 | 2 | 26.1,0.2 | ↑ | ↑↓ |
Glycoprotein (transmembrane) nmb | Gpnmb | 2 | 9.2,0.3 | ↑ | ↑↓ |
Claudin 10 | Cldn10 | 2 | 6.5,0.3 | ↑ | ↑↓ |
Plasminogen activator, urokinase | Plau | 2 | 3,0.4 | ↑ | ↑↓ |
Secreted phosphoprotein 1 | Spp1 | 2,3 | 2.7,0.5 | ↑ | ↑↓ |
Alpha-2-macroglobulin | *A2m | 2 | 46.2,0.4 | ↑ | ↑↓ |
Chemokine (C-C motif) receptor 1 | Ccr1 | 2 | 27.9,0.4 | ↑ | ↑↓ |
Matrix metallopeptidase 9 | Mmp9 | 1,2 | 9.5,0.5 | ↑ | ↑↓ |
Angiopoietin 1 | *Angpt1 | 2 | 9.2,0.2 | ↑ | ↑↓ |
Mucin 1, cell surface associated | Muc1 | 2,3 | 6.8,0.2 | ↑ | ↑↓ |
Heparanase | *Hpse | 2 | 6.3,0.3 | ↑ | ↑↓ |
Megalencephalic leukoencephalopathy with subcortical cysts 1 | Mlc1 | 2 | 4.3,0.4 | ↑ | ↑↓ |
Kinase insert domain protein receptor | *Kdr | 2 | 2.4,0.4 | ↑ | ↑↓ |
Prostaglandin-endoperoxide synthase 2 | Ptgs2 | 1,2,3 | 2.1,0.1 | ↑ | ↑↓ |
Dual specificity phosphatase 1 | Dusp1 | 2 | 6,0.4 | ↓ | ↑↓ |
Cyclin-dependent kinase inhibitor 1C | Cdkn1c | 2 | 2.8,0.1 | ↓ | ↑↓ |
Growth arrest and DNA-damage-inducible, gamma | Gadd45g | 2 | 8,0.4 | ↓ | ↑↓ |
Hepatic nuclear factor 4, alpha | Hnf4a | 2 | 4.5,0.1 | ↓ | ↑↓ |
Runt-related transcription factor 3 | Runx3 | 1,2 | 4.3,0.5 | ↓ | ↑↓ |
Insulin-like growth factor binding protein 3 | Igfbp3 | 1,2 | 2.7,0.4 | ↓ | ↑↓ |
Suppressor of cytokine signaling 3 | *Socs3 | 2 | 2.5,0.1 | ↓ | ↑↓ |
Suppressor of cytokine signaling 1 | *Socs1 | 1,2 | 2.4,0.5 | ↓ | ↑↓ |
Fibroblast growth factor 2 | Fgf2 | 1,2 | 2.1,0.5 | ↓ | ↑↓ |
Fragile histidine triad gene | Fhit | 1,2 | 7.8,0.1 | ↓ | ↑↓ |
Gamma-glutamyltransferase 1 | Ggt1 | 2 | 3.4,0.2 | ↓ | ↑↓ |
Bone morphogenetic protein 7 | Bmp7 | 2 | 3,0.4 | ↓ | ↑↓ |
E74-like factor 1 (ets domain transcription factor) | Elf1 | 2 | 3,0.4 | ↓ | ↑↓ |
CD80 molecule | Cd80 | 2 | 3,0.3 | ↓ | ↑↓ |
Glycine N-methyltransferase | Gnmt | 2 | 2.5,0.4 | ↓ | ↑↓ |
Acyl-Coenzyme A oxidase 1, palmitoyl | Acox1 | 2 | 2.3,0.5 | ↓ | ↑↓ |
- Citation: Xu CS, Zhang SB, Chen XG, Rahman S. Correlation analysis of liver tumor-associated genes with liver regeneration. World J Gastroenterol 2007; 13(24): 3323-3332
- URL: https://www.wjgnet.com/1007-9327/full/v13/i24/3323.htm
- DOI: https://dx.doi.org/10.3748/wjg.v13.i24.3323