Table 1.
Selected Genes Whose Expression Is Upregulated in Rat Bladder Tumors Compared with Normal Bladder Epithelia Identified by Microarray.
| Gene | Accession Number | Description | Fold Change | P |
| Cell cycle-related genes | ||||
| Cdc2a | NM_019296 | CDC2 homolog A* | 2.7* | .0250 |
| Cdc20 | U05341 | CDC20 homolog* | 4.6* | .0040 |
| Cdc23 | BE111697 | CDC23 (cell division cycle 23, yeast, homolog) (predicted)* | 33.3* | .0170 |
| Cdc25B | NM_133572 | CDC25 homolog B | 2.4 | .0007 |
| Cdc42ep5 | AI599324 | CDC42 effector protein (rho GTPase binding) 5 (predicted) | 2.6 | .0027 |
| Cdca1 | BG375704 | Cell division cycle-associated 1 (predicted) | 5.5 | .0125 |
| Cdca2 | AW532628 | Cell division cycle-associated 2 (predicted) | 5.6 | .0456 |
| Cdca3 | BF417638 | Cell division cycle-associated 3 | 6.1 | .0298 |
| Ccna2 | AA998516 | Cyclin A2* | 15.3* | .0028 |
| Ccnb1 | X64589 | Cyclin B1* | 4.8* | .0135 |
| Ccnb2 | AW253821 | Cyclin B2* | 6.5* | .0041 |
| Ccnd1 | X75207 | Cyclin D1* | 8.8* | .0151 |
| Cdkn2a | AF474976 | Cyclin-dependent kinase inhibitor 2A (p16INK4a)* | 8.7* | .0310 |
| Cdkn2c | NM_131902 | Cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4)* | 3.7* | .0005 |
| Cdkn2d | BI290067 | Cyclin-dependent kinase inhibitor 2D* | 2.2* | .0053 |
| Cdkn3 | BE113362 | Cyclin-dependent kinase inhibitor 3 (predicted)* | 21.3* | .0136 |
| Mad2l1 | AW143296 | MAD2 (mitotic arrest deficient, homolog)-like 1 (yeast)* | 2.0* | .0050 |
| Plk1 | U10188 | Polo-like kinase 1 (Drosophila)* | 3.7* | .0218 |
| Plk4 | BE109322 | Polo-like kinase 4 (Drosophila) (predicted)* | 2.5* | .0059 |
| Gadd45b | BI287978 | Growth arrest and DNA damage- inducible 45 β (predicted)* | 2.7* | .0007 |
| Gadd45g | AI599423 | Growth arrest and DNA damage- inducible 45 γ (predicted) | 2.4 | .0106 |
| Gas5 | BF287008 | Growth arrest-specific 5 | 2.3 | .0367 |
| Gas7 | AJ131902 | Growth arrest-specific 7 | 2.3 | .0305 |
| Gap43 | NM_017195 | Growth-associated protein 43 | 2.1 | .0167 |
| Gdf1 | BI289525 | Growth differentiation factor 1 (predicted) | 6.1 | .0769 |
| Bub1 | BF388785 | Budding uninhibited by benzimidazoles 1 homolog* | 11.5* | .0000 |
| Bub1b | BF557145 | Budding uninhibited by benzimidazoles 1 homolog, β | 7.9 | .0074 |
| Myc | NM_012603 | Myelocytomatosis viral oncogene homolog (avian) | 2.5 | .0077 |
| Jundp | NM_053894 2 | Jun dimerization protein 2 | 3.8 | .0017 |
| Dusp6 | NM_053883 | Dual-specificity phosphatase 6* | 2.4* | .0245 |
| Mki67 | AI714002 | Antigen identified by monoclonal antibody Ki-67* | 20.8* | .0010 |
| Small G proteins | ||||
| Racgap1 | AI409259 | Rac GTPase-activating protein 1* | 17.8* | .0146 |
| Rad51 | BI303370 | RAD51 homolog (Saccharomyces cerevisiae)* | 5.1* | .0048 |
| Rem2 | BI296482 | Rad- and gem-related GTP-binding protein 2 | 10.4 | .0045 |
| Rap2a | AW251376 | Rap2A-like protein | 3.6 | .0190 |
| Rap2b | NM_133410 | RAP2B, member of RAS oncogene family | 2.9 | .0185 |
| Rap2ip | AI535169 | Rap2-interacting protein* | 4.8* | .0221 |
| Rin3 | AI706777 | Ras and Rab interactor 3 (predicted) | 4.5 | .0045 |
| Rasgrp1 | BI282819 | RAS guanyl-releasing protein 1* | 2.3* | .0129 |
| Rasgrp2 | AW532114 | RAS guanyl-releasing protein 2 (predicted) | 2.1 | .0247 |
| Arhc | AA891940 | Ras homolog gene family, member C (predicted)* | 2.5* | .0003 |
| Arhd | AA955648 | Ras homolog gene family, member D (predicted)* | 2.1* | .0020 |
| Arhe | AI103572 | Ras homolog gene family, member E | 2.8 | .0158 |
| Rnd1 | AI144754 | Rho family GTPase 1 (predicted) | 5.1 | .0405 |
| Arhgap4 | BE111827 | Rho GTPase-activating protein 4 | 3.3 | .0260 |
| Arhgap8 | AA945062 | Rho GTPase-activating protein 8 | 2.3 | .0025 |
| BG377320 | Rho guanine nucleotide exchange factor (GEF) 17 (predicted) | 2.5 | .0003 | |
| Arhgdib | BF285771 | Rho, GDP dissociation inhibitor (GDI) β (predicted) | 3.7 | .0040 |
| Rock2 | BI303031 | Rho-associated coiled coil forming kinase 2 | 2.7 | .0242 |
| BG378261 | Rhophilin, Rho GTPase binding protein 1 (predicted) | 3.9 | .0128 | |
| Oncogenes and tumor-suppressor genes | ||||
| Akt1 | NM_033230 | V-akt murine thymoma viral oncogene homolog 1 | 1.5 | .0077 |
| Akt3 | NM_031575 | Thymoma viral proto-oncogene 3 | 2.4 | .0255 |
| Nf1 | BM386570 | Neurofibromatosis 1 | 3.1 | .0168 |
| Kit | AI454052 | V-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene | 4.2 | .0079 |
| Maf | NM_019318 | V-maf musculoaponeurotic fibrosarcoma (avian) oncogene | 2.7 | .0024 |
| Mafb | AA900536 | V-maf musculoaponeurotic fibrosarcoma oncogene family, protein B (avian) | 3.1 | .0004 |
| Ect2 | AI578135 | Ect2 oncogene (predicted)* | 12.0* | .0122 |
| Fes | BI289400 | Feline sarcoma oncogene (predicted)* | 3.4* | .0068 |
| Fyn | AI230396 | Fyn proto-oncogene | 2.1 | .0266 |
| Myc | NM_012603 | Myelocytomatosis viral oncogene homolog (avian) | 2.5 | .0077 |
| Ndr4 | BG666709 | N-myc downstream regulated 4 | 2.5 | .0031 |
| BM390283 | Large tumor suppressor 2 (predicted) | 2.3 | .0010 | |
| Apoptosis | ||||
| Birc2 | NM_023987 | Inhibitor of apoptosis protein 1* | 3.3* | .0077 |
| Birc5 | NM_022274 | Baculoviral IAP repeat-containing 5 (Survivin) | 3.6* | .0500 |
| Pawr | U05989 | PRKC, apoptosis, WT1, regulator | 2.0 | .0003 |
| Casp1 | D85899 | Caspase 1* | 2.7* | .0173 |
| Casp11 | NM_053736 | Caspase 11* | 4.7* | .0025 |
| Casp12 | NM_130422 | Caspase 12 | 5.7 | .0010 |
| Pycard | BI282953 | Apoptosis-associated speck-like protein containing a CARD | 2.1 | .0047 |
| Bcl11b | BE116855 | B-cell leukemia/lymphoma 11B (predicted) | 4.0 | .0006 |
| Bcl2a1 | NM_133416 | B-cell leukemia/lymphoma 2 related protein A1* | 5.6* | .0033 |
| Bcl3 | AI411774 | B-cell leukemia/lymphoma 3 (predicted)* | 5.8* | .0059 |
| Bcl6 | AI237606 | B-cell leukemia/lymphoma 6 (predicted)* | 3.6* | .0014 |
| Bok | AI227742 | Bcl-2-related ovarian killer protein* | 2.2* | .0040 |
| Cebpd | NM_013154 | CCAAT/enhancer binding protein (C/EBP), δ | 2.9 | .0002 |
| Tnfsf13 | AA800814 | Tumor necrosis factor (ligand) superfamily, member 13 | 2.5 | .0000 |
| Tnfip6 | AF159103 | Tumor necrosis factor α induced protein 6 | 2.4 | .0135 |
| Tnfrsf11b | NM_012870 | Tumor necrosis factor receptor superfamily, member 11b* | 3.9* | .0012 |
| Tnfrsf12a | BI303379 | Tumor necrosis factor receptor superfamily, member 12a | 5.9 | .0000 |
| BI278479 | Tumor necrosis factor, α-induced protein 2 (predicted) | 2.8 | .0024 | |
| Growth factors and related genes | ||||
| Ctgf | NM_022266 | Connective tissue growth factor* | 7.9* | .0002 |
| BF284634 | Epidermal growth factor-containing fibulin-like extracellular matrix protein 1 | 3.9 | .0015 | |
| Fgf13 | NM_053428 | Fibroblast growth factor 13 | 3.6 | .0007 |
| Fgfbp1 | NM_022603 | Fibroblast growth factor binding protein 1* | 30.2* | .0027 |
| Hgf | NM_017017 | Hepatocyte growth factor | 4.3 | .0022 |
| Hgfac | BE119649 | Hepatocyte growth factor activator | 2.1 | .0130 |
| Hdgfrp3 | BI283829 | Hepatoma-derived growth factor, related protein 3 | 3.5 | .0019 |
| Igf1 | M15481 | Insulin-like growth factor 1 | 21.4 | .0010 |
| Igfbp3 | NM_012588 | Insulin-like growth factor binding protein 3* | 3.2* | .0000 |
| Igfbp4 | BE108969 | Insulin-like growth factor binding protein 4 | 2.1 | .0261 |
| Igfbp7 | AI233246 | Insulin-like growth factor binding protein 7 | 3.0 | .0000 |
| Pdgfrb | BM389426 | Platelet-derived growth factor receptor, β polypeptide* | 2.9* | .0017 |
| Pdgfa | BE100812 | Platelet-derived growth factor, α* | 2.1* | .0044 |
| Pdgfc | NM_031317 | Platelet-derived growth factor, C polypeptide | 3.0 | .0054 |
| Scgf | AI576758 | Stem cell growth factor | 2.2 | .0055 |
| Tgfb1 | NM_021578 | Transforming growth factor, β 1 | 6.6 | .0014 |
| Tgfb2 | NM_031131 | Transforming growth factor, β 2* | 5.9* | .0021 |
| Vegfc | NM_053653 | Vascular endothelial growth factor C | 2.5 | .0039 |
Most of the upregulated genes were small G proteins, apoptosis genes, cell cycle-related genes, oncogenes, and growth factors. Fold change is the ratio of the mean gene expression values of tumors to the mean gene expression values of epithelia from the microarray.
*
The genes were also found to be differentially expressed in mouse bladder tumors.