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Table 2 Main public repositories and their features

From: Transcriptomics and Epigenomics in head and neck cancer: available repositories and molecular signatures

SOURCEArrayExpressGEO (Gene expression omnibus) - NCBI (The National Center for Biotechnology Information)TCGA (The Cancer Genome Atlas)FANTOM5
Linkwww.ebi.ac.uk/arrayexpresswww.ncbi.nlm.nih.gov/geo/summaryportal.gdc.cancer.govfantom.gsc.riken.jp
Repository dataPublic archive of Genomics/Functional Genomics Data all organisms, normal and disease associatedPublic archive of Functional Genomics Data of all organisms, normal and disease associatedPublic dataset of Omics Data of Human CancerInternational consortium of functional annotations of mammalian coding and non coding portion of genome
Submitting authorsAll the researchers, following the MIAME and MINSEQE rulesAll the researchers, following the MIAME and MINSEQE rulesOnly TCGA/Pancancer consortium membersOnly FANTOM5 consortium members
Access for downloadingFreeFreeRequired for downloading controlled-access dataFree
Type of available dataArray- and sequence-based data. Meta-analysis not accepted. Updated dailyArray- and sequence-based data. Meta-analysis not accepted. Updated dailyOmics data generated by TCGA Consortium and Pancancer Atlas. Continuously in progressTranscriptomics data. Updated monthly
Query typesSee Elixir Core Data Resource in Table 3Download analysis (find genes, compare 2 sets of samples, cluster heatmaps, experiment design and value distribution)See tools for querying TCGA in Table 3Visualization tools such as ZENBU, a system for data integration, analysis and visualization of NGS based data