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

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)

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/

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/

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/

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/

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]

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/