Table 1.
Cancer-related, high-throughput data repositories. The databases in Fig. 1B are described with additional information including the number of available data sets, data types, and websites. The number of entries is deemed valid as of 05/02/2016
| Names | Description | Address | Cancer relating data |
|---|---|---|---|
| TCGA | The Cancer Genome Atlas (TCGA): now one of programs organized by newly established NCI’s Center for Cancer Genomics (11) | cancergenome.nih.gov | 34 cancer studies (types), 11,091 samples |
| dbGaP | The database of Genotypes and Phenotypes (dbGaP): archive of genome and phenotype in human | www.ncbi.nlm.nih.gov/gap | 991 datasets |
| SRA | Sequence Read Archive (SRA): raw sequencing files and alignment files from next generation sequencing | www.ncbi.nlm.nih.gov/sra | 1,950 cancer studies |
| cBioPortal | Multi-functional platform: supporting intuitive visualization, literate clinical pie chart, and simple data access (75). TCGA data visualization included. | cbioportal.org | 126 cancer genomics studies, 26,080 samples |
| ICGC | The International Cancer Genome Consortium (ICGC): global-scale cancer projects (16) | dcc.icgc.org/ | 66 cancer projects, 17,867 donors |
| ArrayExpress | An archive of functional genomics data (76) | www.ebi.ac.uk/arrayexpress | 14,974 datasets |
| EGA | The European Genome-phenome Archive (EGA) | www.ebi.ac.uk/ega/home | 1,997 datasets |
| UCSC CGB | UCSC Cancer Genomics Browser (UCSC CGB): supplying interactive heat-map based visualization, and ready-to-use tab-delimited genomics and clinical data download (77). TCGA data visualization included. | genome-cancer.ucsc.edu | 720 datasets |
| GEO | The Gene Expression Omnibus (GEO) (19): a public repository for microarray and next-generation sequencing data sets, and one of the representative repositories. | www.ncbi.nlm.nih.gov/geo | 19,554 datasets |
| ENCODE | The Encyclopedia of DNA Elements (ENCODE) Consortium: decoding functional elements in DNA (17). | www.encodeproject.org | Cancer cell lines available |
| CCLE | The Cancer Cell Line Encyclopedia (CCLE) project: genomics and visualization in about 1,000 cell lines. Drug sensitivity available for the cell lines (78). | www.broadinstitute.org/ccle/home | Genomic characterization of 1,000 cell lines |
| PeptideAtlas | An archive of proteome information (21) | www.peptideatlas.org | 99 datasets |
| PRIDE | PRoteomics IDEntifications (PRIDE) database: protein and peptide identifications, post-translational modifications (22). Mass spectrometry based proteomics data available. | www.ebi.ac.uk/pride/archive | 290 datasets |