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Table 1 Overview of the genetic, epigenetic and molecular information used in this study

From: A Boolean-based systems biology approach to predict novel genes associated with cancer: Application to colorectal cancer

Functional Attribute Role in Cancer Potential application Examples Data source Reference
Cancer associated genes Genes with at least 2 mutations in causally implicated in cancer. Includes oncogenes, tumor suppressor genes Potential drug targets and diagnostic or prognostic markers Oncogenes: BCL2, c-Jun, ERG, ERBB2, RAS, c-MYC, c-SRC
Tumor Suppressor Genes:
RB1, P53, APC, BRCA-1,
BRCA-2
http://www.sanger.ac.uk/genetics/CGP/Census/
http://hprd.org/
Reviews:
(Futreal et al, 2004; Hahn et al, 2002; Mitelman, 2000; Vogelstein et al, 2004)
NA
Non-cancer associated genes There is no previous report of any causal mutation. If cancer association is established, these genes are either potential drug targets and diagnostic or prognostic markers AMN, B3GNTL1, CDC42BPB
S100A9, TRPM6, VNN1, ZIC2
NCBI - Human Genome
http://www.ncbi.nlm.nih.gov/projects/genome/guide/human/
NA
Kinases More than 30% of cancer related genes are kinases and the most common domain that is encoded by cancer genes is the protein kinase domain Drug targets through inhibitors c-Src, c-Abl, RAS, mitogen activated protein (MAP) kinase, phosphotidylinositol-3-kinase (PI3K), AKT, and the epidermal growth factor receptor (EGFR) Human Kinome Consortium http://kinase.com/human/kinome/ [15]
[17, 51]
Excretory - Secretory proteins Malignant tumors secrete increased levels of ES proteins non-invasive diagnostic or prognostic markers for early detection alpha-fetoprotein, CD44, kallikrein 6, kallikrein 10, MIC-1 Secreted Protein Database (SPD)
http://spd.cbi.pku.edu.cn/
[52, 53]
[54]
[55]
Transcription factors Overactivity of TFs at different stages of cancer is well documented and novel treatment strategies have been suggested for targeted inhibition of oncogenic TFs Alternative therapeutic strategy, potential drug targets C-MYB, NF-kappaB, AP-1, STAT and ETS transcription factors Genomatix
http://www.genomatix.de/
[15, 56]
[57]
[58]
DNA Methylation Methylation patterns are altered in cancer cells as shown in hypomethylation of oncogenes and hypermethylation of tumor suppressor resulting in gene silencing or gene inactivation CpG island methylation could be used as a biomarker of malignant cells hMLH1, BRCA1, MGMT, p16(INK4a), p14(ARF), p15(INK4b, DAPK, APAF-1 Human Colon Methylome from [29] [27, 59]
[28]
[60, 61]
Post-translational modifications Key proteins driving oncogenesis, Can undergo PTM Although Phosphoryltion is partially covered in kinases section, other PTMs such as glycosylation and ubiquitination reported to play a role in malignancies, are included separate functional gene attributes.   BRCA1, EGFR, c-Src, c-Abl, RAS, TP53 HPRD http://hprd.org/ [18]
Burger and Seth, 2004)