Table 1. Main characteristic of the selected oncogenomic portals.
| database | Data source | Sites of analyzed cancer 1 | Oncogenomic data | link |
|---|---|---|---|---|
| Oncomine | TCGA, Cancer data from literature | Bd; Br; Bra; Cer; Clr; Eso; HN; Kd; Lng; Lvr; Lymph; Ov; Pnc; also: cancer cell lines | Drug Sensitivity, Cancer histology, clinical outcome, tissue, pathology, subtype, molecular subtype, patient treatment response | https://www.oncomine.org [13, 14] |
| Kaplan-Meier plotter | Cancer data from literature | Br, Ov; Lng; GIST; | survival analyses | http://kmplot.com/analysis [15] |
| Prognoscan | Cancer data from literature | Bd; Bld; Br; Bra; Clr; EA; Eso; HN; Kd; Lng; Lymph; Ov; Prst; Sk; ST; | survival analyses | http://www.abren.net/PrognoScan/[16] |
| STRING | Protein, gene from literature | Gene, gene from literature | Structure | http://string-db.org [17, 18] |
| cBioPortal | AMC, BCCRC, BGI, British Columbia, Broad, Broad/ Cornell, CCLE, CLCGP, Genentech, ICGC, JHU, Michigan, MKSCC, MKSCC/ Broad, NCCS, NUS, PCGP, Pfizer UHK, Riken, Sanger, Singapore, TCGA, TSP, UTokyo, Yale | ACC; Bd; Bld; Br; Bra; Chl; Clr; Eso; HN; Kd; Lng; Lvr; Lymph; MM; Npx; Ov; Pnc; Prst; Sk; ST; Stc; Thr; Utr; also: cancer cell lines | mutations, putative copy number alterations; mRNA expression, protein/ phosphoprotein level; survival analyses | http://www.cbioportal.org/ [19, 20] |
| Tumorscape | Broad Institute | Bd; Bld; Br; Bra; Clr; Eso; GIST; HN; Htp; Kd; Lng; Lvr; Lymph; Msh; Ov; Pnc; Prst; Sk; ST; Stc; Swn; Thr; Utr; also in: cancer cell lines | copy number alterations | http://www.broadinstitute.org/tumorscape/ [21, 22] |
| ICGC | ICGC, TCGA, TARGET | ACC; Bd; Bld; Br; Bra; Chl; Clr; Eso; HN; Kd; Lng; Lvr; Lymph; MM; Npx; Ov; Pnc; Prst; Sk; ST; Stc; Thr; Utr; also: cancer cell lines | simple somatic mutations, copy number somatic alterations, structural somatic mutations, simple germline variants, DNA methylation, gene/ protein expression, miRNA expression, exon junction; epidemiological and clinical data | https://dcc.icgc.org.[73, 74] |
1 List of abbrieviations of cancer sites. In the brackets there are exemplary cancer subtypes included in the portals. ACC – adenoid cystic carcinoma; Bd – bladder; Bld – blood; Bo – bone; Br – breast; Bra – brain; Chl – cholangiocarcinoma; Clr – colorectal; Col – colon; EA – eye and adnexa; EG - endocrine glands; Eso – esophagus; GIST – gastrointestinal; HN – head and neck; Htp – hematopoietic; Kd – kidney; Lng – lung; Lvr – liver and biliary tract; Lymph – Lymphoma; Msh – mesothelioma; Mth – mouth; Nb – neuroblastoma; Npx – nasopharynx; Ov – ovary; Pan – pancancer; Pnc – pancreas; Pnx – pharynx; Prc/Prn - pheochromocytoma and paraganglioma; Prst – prostate; Rc – rectum; Sk – skin; ST – soft tissues; Stc – stomach; Swn – schwannoma; Thm – thymus; Thr – thyroid; Tst – testis; Utr – uterine (cerxix and corpus).