Table 2 Main public repositories and their features
SOURCE | ArrayExpress | GEO (Gene expression omnibus) - NCBI (The National Center for Biotechnology Information) | TCGA (The Cancer Genome Atlas) | FANTOM5 |
|---|---|---|---|---|
Link | ||||
Repository data | Public archive of Genomics/Functional Genomics Data all organisms, normal and disease associated | Public archive of Functional Genomics Data of all organisms, normal and disease associated | Public dataset of Omics Data of Human Cancer | International consortium of functional annotations of mammalian coding and non coding portion of genome |
Submitting authors | All the researchers, following the MIAME and MINSEQE rules | All the researchers, following the MIAME and MINSEQE rules | Only TCGA/Pancancer consortium members | Only FANTOM5 consortium members |
Access for downloading | Free | Free | Required for downloading controlled-access data | Free |
Type of available data | Array- and sequence-based data. Meta-analysis not accepted. Updated daily | Array- and sequence-based data. Meta-analysis not accepted. Updated daily | Omics data generated by TCGA Consortium and Pancancer Atlas. Continuously in progress | Transcriptomics data. Updated monthly |
Query types | See Elixir Core Data Resource in Table 3 | Download analysis (find genes, compare 2 sets of samples, cluster heatmaps, experiment design and value distribution) | See tools for querying TCGA in Table 3 | Visualization tools such as ZENBU, a system for data integration, analysis and visualization of NGS based data |