Table 1.
Main characteristic of the selected oncogenomic portals.
| Database | Data source | Sites of analyzed cancer* | 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.org59,60 |
| 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/PrognoScan62 |
| STRING | Protein, gene from literature | Gene, gene from literature | Structure | http://stringdb.org66,68 |
| 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/67,69 |
| DAVID functional annotation | — | Signal pathway | GO terms, annotation terms, BioCarta & KEGG pathway, interacting proteins, gene-disease associations, protein functional domains and motifs | https://david.ncifcrf.gov/home.jsp70 |
| OncoLnc | TCGA | Bld: Br: Cer: Col: Eso: Gil: Head; Kd; Leuk; Bra; Lvr; Lng; Ov; Panc; Reect; Src; Stm; MM; | Survival analyses | http://www.oncoLnc.org/63 |
| PROGgeneV2 | TCGA, Cancer data from literature | Br; Kd; Bld; Bon; Bra; Col; Heme; Hnc; Liv; Lng; Ov; Panc; Prs; Rect; Skn; Stm; Uter; Cerv; Eso; Eye; Gst; Mstl; Nure; Src; Tym; Tyrd; also: cancer cell lines | Survival analyses | http://watson.compbio.iupui.edu/chirayu/proggene/database/index.php65 |
| Kaplan-Meier plotter | GEO (Affymetrix microarrays only), EGA and TCGA | Br; Gst; Ov; Lng; Liv; | Survival analyses | http://kmplot.com/analysis/61 |
| GEPIA | RNA sequencing expression data from TCGA and the GTEx project | Acc; Blca; Brca; Cesc; Chol; Coad; Dlbc; Esca; Gbm; Hnsc; Kich; Kirc; Kirp; Laml; Lgg; Lihc; Luad; Lusc; Meso; Ov; Paad; Pcpg; Prad; Read; Sarc; Skcm; Stad; Tgct; Thca; Thym; Ucec; Uvm | Survival analysis, Methylation, Annotation, WGS, SNP, Chip, CGHt | http://gepia.cancer-pku.cn/index.html71 |
| R2: Genomics analysis and visualization platform | GEO, TCGA, and GTEx projects | Gli; Kicc; Lug; Lym; Mlym; Mal; Myel; Neur; Ova; Pan; Wil | Survival analysis | https://hgserver1.amc.nl/cgi-bin/r2/main.cgi?&species=hs72 |
*Abbreviations: 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; Blca – bladder urothelial carcinoma; Brca – breast invasive carcinoma; Cesc – cervical squamous cell carcinoma and endocervical adenocarcinoma; Chol – cholangio carcinoma; Coad – colon adenocarcinoma; Dlbc – lymphoid neoplasm diffuse large B-cell lymphoma; Esca –esophageal carcinoma; Gbm – glioblastoma multiforme; Hnsc – head and neck squamous cell carcinoma; Kich – kidney chromophobe; Kirc – kidney renal clear cell carcinoma; Kirp – kidney renal papillary cell carcinoma; Laml – acute myeloid leukemia; Lgg – brain lower grade glioma; Lihc – liver hepatocellular carcinoma; Luad – lung adenocarcinoma; Lusc – lung squamous cell carcinoma; Meso – mesothelioma; Ov – ovarian serous cystadenocarcinoma; Paad – pancreatic adenocarcinoma; Pcpg – pheochromocytoma and paraganglioma; Prad – prostate adenocarcinoma; Read – rectum adenocarcinoma; Sarc – sarcoma; Skcm – skin cutaneous melanoma; Stad – stomach adenocarcinoma; Tgct – testicular germ cell tumor; Thca – thyroid carcinoma; Thym – thymoma; Ucec – uterine carcinoma; Uvm – uveal melanoma; Myel – myeloma; Neur – neuroblastoma; Wil – Wilms.