Table 3.
Potential Biomarkers of BC – Gene Functions and Metabolic Pathways According to Genecards (http://www.genecards.org/) Accessed June 2012. For Each Section, Genes are Listed in Alphabetical Order, According to their Full Name (Column 2)
| Symbol(s) | Full Name | Molecular Function | Metabolic Pathways | Refs |
|---|---|---|---|---|
| Genes Controlling Cell Cycle Regulation | ||||
| CCND1, Bcl1 | Cyclin D1 | Cyclin | Proliferation, G1/S Transition | [88, 164] |
| Cdk2/4 | Cyclin dependent kinase 2 and 4 | Ser/Thr cyclin dependent kinases | Proliferation, G1/S Transition | [82, 83] |
| CCNE1 | Cyclin E1 | Cyclin | Proliferation, G1/S Transition | [88] |
| TP21, p21, CIP1, WAF1, CDKN1A | Cyclin-dependent kinase inhibitor 1A | Protein Repressor | Proliferation, G1/S Checkpoint | [81] |
| TP27, p27, CDKN4, CDKN1B | Cyclin-dependent kinase inhibitor 1B | Protein Repressor | Proliferation, G1/S Checkpoint | [76, 77, 82, 83] |
| TP14, p14, NK4a, INK4, ARF, TP16, p16, CDKN2A | Cyclin-dependent kinase inhibitor 2A | Protein Repressor | Proliferation | [171, 187-189] |
| GATA2, NFE1B | GATA binding protein 2 | Transcriptional Activator | Cell Proliferation | [183] |
| E2F3 | E2F transcription factor 3 | Transcription Factor | Cell Proliferation | [162] |
| EZH2, ENX1, KMT6 | Enhancer of zeste homolog 2 | Transcriptional Repressor | Cell Differentiation | [203] |
| EOMES; TBR2 | Eomesodermin | Transcriptional Activator | Embryo Development | [207] |
| FGFR3 | Fibroblast growth factor receptor 3 | Tyrosine Kinase | Cell Cycle Control; Angiogenesis | [131, 132, 217] |
| GDF-9 | Growth differentiation factor-9 | Growth Factor | Oncosuppressor; Cell Proliferation | [202] |
| HOXA9 | Homeobox A9 | Transcription Factor | Cell Differentiation; Morphogenesis | [207] |
| ID-1, ID1 | Inhibitor of DNA binding 1 | HLH-Protein | Cell Proliferation and Senescence; Cell Differentiation | [165] |
| KRT2A/6B/6C/7/8/10/19/20 | Keratins 2A/6B/6C/7/8/10/19/20 | Intracellular Structure | Cell Activation and Proliferation | [172, 207, 208] |
| KRTAP13-1, KRTAP19-2, KRTAP20-2 | Keratin-associated proteins 13-1, 19-2, 20-2 | Intracellular Structure | Cell Activation and Proliferation | [208] |
| Nkx.28, NKX2-8 | NK2 homeobox 8 | Unknown | Control of p27, cyclin D1, FOXO3a | [86] |
| PLK1 | Polo-like kinase 1 | Ser/Thr protein kinase | Control of Mitosis | [90] |
| POU4F2 | POU class 4 homeobox 2 | Transcription Factor | Cell Differentiation (Putative) | [207] |
| Rb, RB1 | Retinoblastoma | Transcription Repressor | Control of G0/G1 Transition | [89] |
| RARB, HAP, NR1B2 | Retinoic acid receptor b2 | Hormone Receptor | Cell Differentiation | [173] |
| RUNX3, AML2, CBFA3 | Runt-related transcription factor 3 | Transcription Factor | Activation and Repression of Transcription | [193, 196] |
| SOX9, CMD1 | Sex determining region Y-box 9 | Transcription Factor | Chondrogenesis | [194] |
| TP53, p53 | Tumor protein p53 | Transcription Factor | Proliferation, Apoptosis, Angiogenesis | [73, 76-78] |
| TP63, p63 | Tumor protein p63 | Transcriptional Activator/Repressor | Proliferation, Apoptosis | [75] |
| TWIST, TWIST1, ACS3, BPES2 | Twist homolog 1 | Transcription Factor | Cell Differentiation | [214] |
| TBX2 | T-box 2 | Unknown | Cell Differentiation | [183] |
| TBX3 | T-box 3 | Transcriptional Repressor | Cell Differentiation | [183] |
| AKT1, AKT, RAC | v-akt murine thymoma viral oncogene homolog 1 | Ser-Thr protein kinase | Cell Proliferation; Cell Survival; Angiogenesis | [137, 138, 166] |
| c-myc, MYC | v-myc myelocystomatosis viral oncogene homolog | Regulation of Gene Transcription | Cell Proliferation | [161] |
| Genes Controlling Apoptosis | ||||
| cIAP1, BIRC2, RNF48 | Baculoviral IAP repeat containing 2 | Protein Inhibitor | Inhibition of Apoptosis | [99] |
| BIRC5, Survivin | Baculoviral IAP repeat containing 5 | Protein Inhibitor | Inhibition of Apoptosis; Cell invasion; Regulator of Mitosis | [96-98] |
| Bcl-2, PPP1R50 | B-cell CLL/lymphoma 2 | Control of Mitochondrial Membrane Permeability | Inhibition of Apoptosis | [92, 215] |
| BNIP3 | BCL2/adenovirus E1B interacting protein 3 | Calcium Repartitioning | Cell Survival | [116] |
| c-FLIP, CFLAR | CASP8 and FADD-like apoptosis regulator | Protein Inhibitor | Apoptosis Resistance | [100] |
| CASP3, CPP32, Yama | Caspase-3 | Cysteine-Aspartic Protein Peptidase | Activation of Apoptosis | [92, 93] |
| DAPK | Death Associated Protein kinase 1 | Serine-Threonine Kinase | Apoptosis; Cell Survival | [177, 188, 215, 216] |
| CD95L, FASLG | Fas ligand TNF superfamily 6 | Ligand for Fas | Activation of Apoptosis | [94, 100] |
| FOXO3a, AF6q21 | Forkhead box 3A | Transcription Factor | Activation of Apoptosis | [86] |
| GDF15, MIC1, PLAB | Growth Differentiation factor 15 | Unknown | Activation of Apoptosis | [206] |
| PMF1 | Polyamine-Modulated Factor 1 | Polyamine Homeostasis | Control of Cell Growth and Death | [212] |
| RASSF1A | Ras association domain family member 1 | Protein Inhibitor | Cell Proliferation Inhibitor | [187, 189-191, 215] |
| TMEFF2, tomoregulin-2 | Transmembrane protein with EGF-like and follistatin-like domains 2 | Activator of Phosphorilation | Cell Survival | [206] |
| DR4, TNFRSF10A | Tumor necrosis factor receptor superfamily 10A | Death Receptor | Activation of Apoptosis | [101] |
| DR5, TNFRSF10B | Tumor necrosis factor receptor superfamily 10B | Death Receptor | Activation of Apoptosis | [101] |
| TRAIL, TNFRSF10C | Tumor necrosis factor receptor superfamily 10C | Protein Inhibitor | Apoptosis Resistance | [101] |
| Fas, APT1, TNFRSF6 | Tumor necrosis factor receptor superfamily 6 | Death Receptor | Activation of Apoptosis | [94, 95, 205] |
| DR3, TNFRSF25 | Tumor necrosis factor receptor superfamily member 25 | Death Receptor | Activation of Apoptosis | [205] |
| Genes Controlling Angiogenesis | ||||
| bFGF, FGF2 | Basic fibroblast growth factor | Heparin Binding | Pro-Angiogenesis; Mitogen | [102] |
| EDNRB | Endothelin receptor type B | G-protein-coupled Receptor | Regulation of Angiogenesis | [204] |
| Prolidase, PEPD | Peptidase D | Metalloproteinase | Collagen Metabolism; Pro-angiogenesis | [169] |
| THBS1, TSP1 | Thrombospondin-1 | Adhesive Glicoprotein; Heparin Binding | Inhibitor of Angiogenesis | [102] |
| VEGF | Vascular Endothelial Growth Factor | Signaling Protein | Cell Replication and Migration; Inhibition of Apoptosis | [103, 104] |
| Genes Controlling Cell-Cell Interactions | ||||
| ADAM12 | ADAM metallopeptidase Domain 12 | Metalloproteinase | Multinucleate Cell Formation | [127] |
| ADAM17 | ADAM metallopeptidase Domain 17 | Metalloproteinase | Release of Cell Surface Proteins | [127] |
| ADAM28 | ADAM metallopeptidase Domain 28 | Metalloproteinase | Cell Adhesion | [126] |
| APC | Adenomatous Polyposis Coli | Antagonist of Wnt Pathway | Cell Migration and Adhesion; Apoptosis | [191, 204] |
| AR, DHTR, SBMA, AIS | Androgen Receptor | Steroid Hormone Receptor | Cell Growth, Differentiation and Function | [129] |
| Annexin10, ANXA10 | Annexin A10 | Unknown | Cell Migration | [121, 122] |
| APOE, LPG | Apolipoprotein E | Catabolism of Lipoproteins | Cell Function | [130] |
| BLCA-4 | Bladder Cancer A4 | Transcription Factor | Metastasis Formation | [167, 168] |
| BAMBI | BMP and activin membrane-bound inhibitor homolog | Signal Receptor | Metastasis invasion; Cell Movement | [201] |
| LASS2 | Ceramide synthase 2 | Sphingolipid Synthesis (Putative) | Metastasis Suppressor | [123] |
| COL1A2 | Collagen Type 1a2 | Collagen | Extracellular Matrix Formation | [219] |
| CTTN, EMS1 | Cortactin | Unknown | Cytoskeletal Organization; Regulation of Cell-Cell Junctions; Regulation of Invasiveness | [124] |
| CDH1 | E-cadherin | Calcium-Dependent Membrane Protein | Cell Adhesion | [128, 129, 184] |
| ERa, ESR1 | Estrogen Receptor Alpha | Steroid Hormone Receptor | Cell Growth, Differentiation and Function | [129] |
| FGB | Fibrinogen Beta Chain Precursor | Polymerization of Monomers | Cell Adhesion | [130] |
| HYAL-1, LUCA1, NAT6 | Hyaluronoglucosaminidase 1 | Degradation of Hyaluronic Acid | Cell Proliferation, Migration and Differentiation | [218] |
| MAPK | Mitogen-activated protein kinase family | Ser-Thr kinase | Cell Growth, Adhesion, Survival and Differentiation | [137, 138] |
| NID2 | Nidogen2 | Membrane Glycoprotein | Cell Adhesion | [214] |
| PTEN, BZS, MMAC1, | Phosphatase and tensin honolog | Protein and Lipid Phosphatase | Cell Migration Inhibition | [178] |
| PIK3CA | Phosphoinositide-3-kinase catalytic alpha polypeptide | Lipid Kinase | Cell Growth, Survival, Proliferation, Motility and Morphology | [119, 137, 138] |
| PLCG1 | Phospholipase C, g1 | Phospholipase | Actin Organization; Cell Migration | [137, 138] |
| PFN1 | Profilin-1 | Actin Binding | Cytoskeletal Organization | [125] |
| PRKCI | Protein kinase C | Ser-Thr kinase | Modulation of Membrane Structure | [137, 138] |
| RIN1 | Ras and Rab interactor 1 | Ras Effector Protein | Cytoskeletal Remodeling | [115] |
| RAS | Rat sarcoma viral oncogene family | GTPase | Activation of Mitosis | [114] |
| SFRP | Secreted frizzled receptor protein family | Protein Receptor | Metastasis invasion; Cell Movement | [199, 200] |
| SERPINA1 | Serpin peptidase inhibitor 1 | Alpha-1 Antitrypsin | Inhibition of Elastase | [130] |
| STAT1, STAT91 | Signal transducer and activator of transcription 1 | Signal Transducer | Response to Growth Factors | [139] |
| TIMP-3 | TIMP metallopeptidase inhibitor 3 | Proteinase | Cell Remodeling | [213] |
| TSC1, LAM, hamartin | Tuberous sclerosis 1 | Protein Inhibitor | Inhibition of Nutrient-Mediated Cell Growth | [120] |
| UPK | Uroplakin | Integral Membrane Proteins | Cytoskeleton Regulation | [107] |
| HER2, ERBB2 | v-erb-b2 erythroblastic leukemia viral oncogene homolog 2 | Epidermal Growth Factor Receptor; Tyrosine Kinase | Activation of Mitosis | [108, 109] |
| Src, ASV | v-src sarcoma viral oncogene homolog | Tyrosine Kinase | Cell Proliferation, Survival and Migration | [137, 138] |
| Other Genes | ||||
| hOGG1 | 8-oxoguanine DNA glycosilase | Glycosylase | DNA Base Excision Repair | [142] |
| C10orf116 | Chromosome 10 open reading frame 116 | Unknown | Unknown | [172] |
| CYP1B1 | Cytochrome P450 1B1 | Oxidation | Chemical Modification of Various Compounds; Detoxification | [151] |
| ERCC1 | Excision repair cross-complementing rodent repair deficiency, group 1 | Endonuclease | DNA Nucleotide Excision Repair | [143] |
| ERCC2, XPD, TFIIH | Excision repair cross-complementing rodent repair deficiency, group 2 | Helicase | Double-Stranded DNA Breaks Repair | [142, 144] |
| GSTM1 | Glutathione S-transferase mu 1 | Chemical Conjugation | Detoxification | [149, 150] |
| GSTP1 | Glutathione S-transferase pi 1 | Chemical Conjugation | Detoxification | [149, 150] |
| GSTT1 | Glutathione S-transferase theta 1 | Chemical Conjugation | Detoxification | [149, 150] |
| HMGB1, SBP1 | High mobility group box 1 | DNA Bending | DNA Transcription and Repair | [140] |
| SIRT2 | Histone Deacetylase | Chromatin Remodeling | Gene Expression Control | [124] |
| HDAC6 | Histone Deacetylase 6 | Chromatin Remodeling | Gene Expression Control | [124] |
| LRG1 | Leucine-rich alpha-2-glycoprotein 1 | Unknown | Unknown | [130] |
| MTHFR | Methylenetetrahydrofolate reductase NAD(P)H | Reductase | Nucleotide Biosynthesis | [141] |
| NBS1, NBN | Nibrin | DNA Damage Signaling | Double-Stranded DNA Breaks Repair | [144] |
| PARP1, PPOL | Poly(ADP-ribose) polymerase 1 | DNA Polymerase | Base Excision DNA Repair | [146] |
| SYNPO2, Myopodin | Synaptopodyn 2 | Actin-binding Protein | Unknown | [211] |
| UGT | UDP glucuronosyltransferase family | Chemical Modification of xenobiotics | Detoxification | [148] |
| VIM | Vimentin | Type III Intermediate Filament | Cell Structure | [206] |
| XPC, Rad4, P125 | Xeroderma pigmentosum, group C | DNA Bending | Nucleotide Excision DNA Repair | [144] |
| XRCC3 | X-ray repair complementing defective repair in Chinese hamster cells 3 | Unknown | Double-Stranded DNA Breaks Repair by Homologous Recombination | [145] |
| ZIC4 | Zic family member 4 | DNA Binding | Unknown | [183] |
| ZNF154 | Zinc finger protein 154 | Transcriptional Regulation (Putative) | Unknown | [191] |