Table 1.
Summary of Large Data Repositories for Omics Analytics
| Repository | Data type | Link |
|---|---|---|
| Gene Expression Omnibus | Gene expression, noncoding RNA profiling, epigenetics, genome variation profiling | www.ncbi.nlm.nih.gov/geo/ |
| ENCODE | Epigenetics, gene expression, computational predictions | www.encodeproject.org |
| ArrayExpress | DNA sequencing, gene and protein expression, epigenetics | www.ebi.ac.uk/arrayexpress/ |
| European Genome-Phenome Archivea | Various omics with phenotype data (biomedical studies) | https://ega-archive.org |
| PRoteomics IDEntifications (PRIDE), ProteomeXchange | Proteomics, protein expression, post-translational modifications |
www.ebi.ac.uk/pride/archive/ http://www.proteomexchange.org/ |
| 1000 Genomes | Genome sequences, sequence variants | www.internationalgenome.org |
| MetaboLights | Metabolomics | www.ebi.ac.uk/metabolights/ |
| GTExa | Gene expression (microarrays and RNA-seq), genome sequences | www.gtexportal.org |
| National Institutes of Health/National Cancer Institute (NIH/NCI) Genomic Data Commons | Gene expression, epigenetics, miRNA-seq (focus on cancer) | https://portal.gdc.cancer.gov |
| NIH dbGaPa | Genotypes, gene expression, epigenetics, phenotypes | https://www.ncbi.nlm.nih.gov/gap |
| cBioPortal | Focused on cancer, contains data on gene copy numbers, gene and protein expression, DNA methylation, and clinical data | http://www.cbioportal.org |
| Single Cell Expression Atlas | Single-cell gene expression (RNA-seq) | https://www.ebi.ac.uk/gxa/sc/ |
| RIKEN SCPortalen | Single-cell gene expression (RNA-seq) | http://single-cell.clst.riken.jp/ |
a
Needs granted access for individual-level data.