Table 2.
Differential expressions of important genes
| Coordinate | Genbank | Gene Name | 1 | 2 | 3 | 4 | 5 | 6 |
| BC/BA | NCL/BC | HCC/NCL | HCC/BC | HCC/BA | HCC/C | |||
| Oncogenes & tumor suppressors (1/57, 1.8%) | ||||||||
| A1i | X12795 | v-erbA related protein 3 (EAR3) | ↑(3.56) | ↑(7.45) | ↑(4.80) | |||
| Cell Cycle Regulators (1/41, 2.4%) | ||||||||
| A6i | L26584 | cell division cycle 25 homolog (CDC25) | ↑(3.43) | ↑(5.92) | ||||
| Ion channels & transport proteins (0/3) | ||||||||
| Modulators, effectors & intracellular transducers (5/88, 5.7%) | ||||||||
| B1f | M62424 | thrombin receptor (TR) | ↓(0.15) | ↑(5.64) | ↑(10.75) | ↑(6.52) | ||
| B1l* | X74764 | neurotrophic tyrosine kinase | ↑(5.50) | ↑(2.63) | ↑(14.05) | ↑(25.36) | ||
| receptor-related 3 | ||||||||
| B2j | D21878 | bone marrow stromal antigen 1 (BST-1) | ↓(0.15) | ↑(11.14) | ↑(3.40) | |||
| B4l | U07707 | epidermal growth factor receptor | ↓(0.40) | ↑(2.87) | ↑(2.18) | |||
| substrate 15 (EPS15) | ||||||||
| B5m* | M65066 | cAMP-dependent protein kinase type I | ↓(0.02) | ↑(4.03) | ↑(11.35) | ↑(51.59) | ||
| beta regulatory subunit (PRKAR1B) | ||||||||
| Stress response proteins (1/7, 14.3%) | ||||||||
| B7m | M11717 | heat shock 70-kDa protein 1 (HSP70.1) | ↓(3.54) | ↑(0.26) | ↑(0.26) | ↑(0.17) | ||
| Apoptosis-associated proteins (15/64, 23.4%) | ||||||||
| C1g | M14694 | p53 cellular tumor antigen | ↓(0.35) | ↓(0.10) | ||||
| C1n | L07414 | TNF-related activation protein (TRAP) | ↓(0.42) | ↓(0.24) | ||||
| C3c | M25627 | glutathione S-transferase A1 (GSTA1) | ↓(0.29) | ↓(0.23) | ||||
| C3j | M13228 | N-myc proto-oncogene | ↑(181.47) | ↓(0.30) | ↑(148.98) | ↓(0.18) | ||
| C3k | U25994 | receptor (TNFRSF)-interacting | ↑(4.61) | ↓(0.25) | ↓(0.06) | |||
| serine-threonine kinase 1 (RIPK1) | ||||||||
| C3n | L11015 | tumor necrosis factor C (TNFC) | ↓(0.24) | ↓(0.08) | ||||
| C4c* | U15172 | NIP1 (NIP1) | ↓(0.08) | ↓(0.16) | ↓(0.20) | |||
| C4d* | U15174 | BCL2/adenovirus E1B 19-kDa- | ↓(0.31) | ↓(0.34) | ↓(0.21) | |||
| interacting protein 3 (BNIP3) | ||||||||
| C4f | U23765 | BCL2 homologous | ↓(0.28) | ↓(0.12) | ||||
| antagonist/killer 1 (BAK1) | ||||||||
| C4h | U29680 | BCL2-related protein A1 (BCL2A1) | ↑(8.19) | ↓(0.16) | ↓(0.09) | |||
| C4k | U45880 | inhibitor of apoptosis protein 3 (IAP3) | ↑(4.53) | ↓(0.42) | ↓(0.23) | |||
| C4m* | U57059 | TNF-related apoptosis inducing | ↓(0.26) | ↓(0.20) | ↓(0.40) | |||
| ligand (TRAIL) | ||||||||
| C5c | Y09392 | WSL protein+TRAMP+Apo-3+ | ↓(0.39) | ↓(0.20) | ||||
| death domain receptor 3 (DDR3) | ||||||||
| C5f | U39613 | cysteine protease ICE-LAP3 | ↓(0.13) | ↓(0.03) | ||||
| C5h | U71364 | cytoplasmic antiproteinase 3 (CAP3) | ↑(44.85) | ↓(0.28) | ↓(0.13) | |||
| DNA synthesis, repair & recombinant proteins (15/34, 44.1%) | ||||||||
| C5k* | L07540 | replication factor C 36-kDa | ↓(0.24) | ↑(6.73) | ↓(0.26) | ↓(0.26) | ↓(0.17) | |
| subunit (RFC36) | ||||||||
| C6a | M30938 | nuclear factor IV | ↓(0.25) | ↓(0.07) | ||||
| C6b | M31899 | xeroderma pigmentosum group B | ↓(0.06) | ↓(0.04) | ||||
| complementing protein (XPB-ERCC3) | ||||||||
| C6c | M32865 | 70-kDa thyroid autoantigen (TLAA) | ↓(0.44) | ↓(0.20) | ||||
| C6e | M63488 | replication protein A 70-kDa | ↓(0.25) | ↓(0.07) | ||||
| subunit (RPA70) | ||||||||
| C6l | J04088 | DNA topoisomerase II alpha (TOP2A) | ↑(4.00) | ↓(0.33) | ↓(0.30) | |||
| C7a | M13194 | excision repair cross-complementing | ↓(0.26) | ↓(0.09) | ||||
| rodent repair deficiency | ||||||||
| complementation group 1 (ERCC1) | ||||||||
| C7b | M13267 | cytosolic superoxide dismutase 1 (SOD1) | ↓(0.39) | ↓(0.24) | ||||
| C7c | U07418 | colon cancer nonpolyposis type | ↓(0.30) | ↓(0.10) | ||||
| 2 protein (COCA2) | ||||||||
| C7d* | D21090 | UV excision repair protein RAD23 | ↓(0.26) | ↓(0.44) | ↓(0.08) | |||
| homolog B (hHR23B; XPC repair- | ||||||||
| complementing complex 58-kDa protein) | ||||||||
| C7g | S40706 | growth arrest & DNA damage-inducible | ↓(0.29) | ↓(0.15) | ||||
| protein 153 (GADD153) | ||||||||
| C7i | U12134 | DNA damage repair & recombination | ↑(6.02) | ↓(0.27) | ↓(0.12) | |||
| protein 52 homolog (RAD52) | ||||||||
| C7k | U63139 | DNA damage repair & recombination | ↓(0.18) | ↓(0.08) | ||||
| protein 50 homolog (RAD50) | ||||||||
| C7m | X84740 | DNA ligase III (LIG3) | ↑(4.23) | ↓(0.21) | ↓(0.08) | |||
| C7n | X90392 | muscle-specific DNase I-like (DNL1L) | ↓(5.36) | ↓(0.22) | ↓(0.12) | |||
| Transcription factors & DNA-bingding proteins (8/98, 8.2%) | ||||||||
| D3a | D26155 | SWI/SNF-related matrix-associated | ↓(0.19) | ↑(3.85) | ↑(4.58) | ↑(2.55) | ||
| actin-dependent regulator of chromatin | ||||||||
| subfamily A member 2 (SMARCA2) | ||||||||
| D4b* | M36542 | octamer-binding transcription | ↑(2.64) | ↑(8.32) | ↑(7.33) | ↑(3.30) | ||
| factor 2 (OCT2) | ||||||||
| D4e | M62810 | mitochondrial transcription | ↑(8.04) | ↑(25.07) | ||||
| factor 1 (MTTF1) | ||||||||
| D4j | M76541 | transcriptional repressor protein | ↓(0.32) | ↑(2.73) | ↑(3.74) | ↑(3.10) | ||
| yin & yang 1 (YY1) | ||||||||
| D5a* | M83234 | nuclease-sensitive element | ↑(2.59) | ↑(3.24) | ↑(2.75) | ↑(5.21) | ||
| DNA-binding protein (NSEP) | ||||||||
| D5f | M96824 | nucleobindin 1 (NUCB1) | ↓(0.24) | ↑(2.64) | ↑(3.00) | ↑(2.37) | ||
| D6h* | U10324 | nuclear factor NF90 | ↑(3.69) | (2.34) | ↑(2.90) | |||
| D6l | U14575 | activator of RNA decay (ARD-1) | ↑(72.46) | ↑(2.53) | ↑(93.75) | |||
| Growth factor & chemokine receptors (1/25, 4.0%) | ||||||||
| E1h | L06623 | endothelin receptor type B (ETB) | ↓(0.37) | ↑(4.46) | ↑(2.07) | ↑(2.78) | ||
| Interleukin & interferon receptors (0/18) | ||||||||
| Hormone receptors (0/4) | ||||||||
| Neurotransmitter receptors (0/11) | ||||||||
| Cell surface antigens & adhesion proteins (3/40, 7.5%) | ||||||||
| E5l | M23197 | myeloid cell surface CD33 antigen | ↑(6.68) | ↑(5.75) | ↑(3.26) | |||
| E6f* | M74777 | dipeptidyl peptidase IV (DPP IV); | ↓(0.32) | ↓(0.36) | ↓(0.28) | |||
| T-cell activation CD26 | ||||||||
| E7b | M35198 | integrin beta 6 (ITGB6) | ↑(5.44) | ↓(0.44) | ↓(0.36) | |||
| Growth factors, cytokines & chemokines (20/64, 31.3%) | ||||||||
| F1f | X03438 | granulocyte colony-stimulating | ↑(8.95) | ↑(3.32) | ↓(0.05) | ↓(0.18) | ↓(0.06) | |
| factor (GCSF) | ||||||||
| F1j* | M16552 | thrombomodulin (THBD) | ↓(0.10) | ↓(0.24) | ↓(0.23) | |||
| F2a | D16431 | hepatoma-derived growth factor (HDGF) | ↓(0.39) | ↓(0.28) | ||||
| F2c | J04130 | T-cell activation protein 2 (AT2) | ↓(0.17) | ↓(0.20) | ||||
| F2e | K03515 | neuroleukin (NLK) | ↑(9.09) | ↓(0.40) | ↓(0.26) | |||
| F2f | L12260 | neuregulin 1 (NRG1) | ↑(21.23) | ↓(0.10) | ↑(3.76) | ↓(0.13) | ||
| F2g | L12261 | heregulin-beta3 | ↑(6.10) | ↓(0.10) | ↓(0.14) | |||
| F2h | L36052 | thrombopoietin (THPO) | ↑(7.26) | ↓(0.04) | ↓(0.24) | ↓(0.06) | ||
| F2m | M22491 | bone morphogenetic protein 3 (BMP3) | ↓(0.05) | ↓(0.08) | ||||
| F3a | M24545 | small inducible cytokine subfamily | ↓(0.36) | ↓(0.34) | ||||
| A member 2 (SCYA2) | ||||||||
| F3d | M30704 | amphiregulin (AR) | ↑(3.69) | ↓(0.17) | ↓(0.41) | ↓(0.12) | ||
| F3i | M57502 | small inducible cytokine subfamily | ↓(0.22) | ↓(0.27) | ||||
| A member 1 (SCYA1) | ||||||||
| F3l | M60718 | hepatocyte growth factor (HGF) | ↓(0.20) | ↓(0.30) | ||||
| F4c | M74178 | hepatocyte growth factor-like protein | ↓(0.31) | ↑(5.11) | ↑(4.62) | ↓(2.28) | ||
| F4e | M92934 | connective tissue growth factor (CTGF) | ↑(3.86) | ↑(6.00) | ↓(0.30) | ↑(5.44) | ↓(0.24) | |
| F4h | U43142 | vascular endothelial growth | ↑(8.75) | ↑(3.82) | ↓(0.14) | ↑(4.81) | ↓(0.15) | |
| factor C (VEGFC) | ||||||||
| F4i | X02530 | small inducible cytokine subfamily | ↑(5.60) | ↑(4.14) | ↓(0.14) | ↑(3.17) | ↓(0.15) | |
| B member 10 (SCYB10) | ||||||||
| F4k | X06234 | calgranulin A (CALA) | ↓(0.21) | ↓(0.21) | ||||
| F4n | X51943 | AFGF + HBGF-1 + ECGF-beta | ↓(0.10) | ↓(0.19) | ||||
| F5e | X79929 | OX40 ligand (OX40L) | ↑(5.42) | ↓(0.11) | ↓(0.31) | ↓(0.09) | ||
| Interleukins & interferons (12/20, 60.0%) | ||||||||
| F5j | J04156 | interleukin 7 (IL7) | ↑(3.62) | ↓(0.25) | ↓(0.27) | |||
| F5k | A14844 | interleukin 2 (IL2) | ↑(11.82) | ↓(0.14) | ↓(0.16) | ↓(0.13) | ||
| F5l | X02851 | interleukin 1 alpha (IL1-alpha) | ↓(0.19) | ↓(0.24) | ||||
| F5n | M14743 | interleukin 3 (IL3) | ↑(11.18) | ↓(0.08) | ↓(0.06) | |||
| F6a | M13982 | interleukin 4 (IL4) | ↑(2.87) | ↓(0.26) | ↓(0.22) | |||
| F6b* | X04602 | interleukin 6 (IL6) | ↑(3.37) | ↑(2.73) | ↑(9.47) | ↑(12.41) | ||
| F6d | M28622 | interferon beta 1 (IFN-beta 1) | ↓(0.17) | ↓(0.16) | ||||
| F6g | L06801 | interleukin 13 (IL13) | ↓(0.20) | ↑(5.04) | ↑(5.90) | ↓(2.36) | ||
| F6i | M57765 | interleukin 11 (IL11) | ↑(4.15) | ↓(0.11) | ↓(0.40) | ↓(0.10) | ||
| F6j | M65290 | interleukin 12 beta subunit (IL12-beta) | ↑(2.71) | ↓(0.19) | ↓(0.18) | |||
| F6k | M65291 | interleukin 12 alpha subunit | ↑(3.78) | ↓(0.17) | ↓(0.14) | |||
| (IL12-alpha) | ||||||||
| F6l | U14407 | interleukin 15 (IL15) | ↑(3.36) | ↓(0.24) | ↓(0.30) | |||
| Hormones (7/14, 50.0%) | ||||||||
| F7d | A06925 | prorelaxin H2 (RLN2) | ↓(0.23) | ↓(0.16) | ||||
| F7f | J04040 | glucagon (GCG) | ↑(5.75) | ↓(0.17) | ↓(0.12) | |||
| F7i | M31159 | insulin-like growth factor-binding | ↓(0.35) | ↓(0.35) | ||||
| protein 3 ( IGFBP3) | ||||||||
| F7j | M68867 | cellular retinoic acid-binding | ↑(2.84) | ↓(0.27) | ↓(0.23) | |||
| protein II (CRABP2) | ||||||||
| F7l | X58022 | corticotropin-releasing | ↑(5.00) | ↑(2.97) | ↓(0.12) | ↓(0.36) | ↓(0.16) | |
| factor-binding protein | ||||||||
| F7m | U08098 | estrogen sulfotransferase (STE; EST) | ↑(5.62) | ↑(3.44) | ↑(12.98) | |||
| F7n | X54469 | preprotachykinin beta (beta-PPT) | ↑(15.57) | ↓(0.07) | ↓(0.21) | ↓(0.09) | ||
| Total amount | 89/588, 15.1% | 32 | 36 | 70 | 29 | 20 | 83 | |
| Up-regulation | 20(62.5) | 35(97.2) | 5(7.1) | 18(62.1) | 13(65.0) | 15(18.1) | ||
| Down-regulation | 12(37.5) | 1(2.8) | 65(92.9) | 11(37.9) | 7(35.0) | 68(81.9) | ||
1 BA: liver tissue from animals before AFB1 treatment (0th week of the experiment). BC: liver tissue from the same HCC animals after AFB1 treatment for 30 weeks. HCC: hepatocellular carcinoma tissue from the same animal after AFB1 treatment. NCL: HCC-surrounding non-cancerous liver tissues from the same HCC animal. C: liver tissue from untreated animals taken at the time when HCC developed in AFB1 treated animals. 2 The numbers followed the name of functional classes are the amount of the important genes identified in this class and their percentage. 3 ↑: up-regulation; ↓: down-regulation. The numbers followed are the averages of the two checked samples. 4 *: Genes might be of more importance.