Table 1.
General omics databases
| Name | Description | Main features |
|---|---|---|
| Genomics | ||
| GeneCards (http://www.genecards.org/) | Detailed information on all annotated and predicted human genes | Contains >152 000 GeneCards genes |
| Gene-centric data from >100 Web sources from all kind of omics | ||
| Very detailed description of genes (aliases, compounds, proteins, domains, expression, related publications, transcripts, pathways) | ||
| Online Mendelian Inheritance in Man (http://www.omim.org/) | Comprehensive, authoritative compendium of human genes and genetic phenotypes | >15 000 genes |
| Information on all known Mendelian disorders | ||
| Relationship between phenotype and genotype | ||
| Transcriptomics | ||
| Gene Expression Omnibus (GEO) (http://www.ncbi.nlm.nih.gov/gds) | Repository for gene expression datasets supplied by researchers | 3848 array and sequence-based datasets |
| Common data submission procedures ensure good data quality | ||
| Tools for data analysis and visualization are provided | ||
| ArrayExpress (https://www.ebi.ac.uk/arrayexpress/) | Functional genomics archive | 60 054 high-throughput experiments |
| Stores both processed and raw data | ||
| Standardized data submission process, frequent updates, connected with GEO | ||
| Expression Atlas (https://www.ebi.ac.uk/gxa/) | Similar to GEO but with fewer datasets that are more focused on baseline experiments | 1572 datasets |
| Two components: Baseline Atlas for expression in ‘normal’ conditions and differential Atlas for experimental expression data | ||
| miRBase (http://www.mirbase.org) | Detailed information on all published and annotated miRNAs | 28 645 entries of miRNAs from 223 species |
| DIANA tools (http://diana.imis.athena-innovation.gr) | Web tool dedicated to miRNA studies | miRNA target identification, and pathway analysis |
| Published validated miRNA–gene interactions | ||
| Automated pipelines to analyse user data | ||
| miRNA-related publication search | ||
| Proteomics | ||
| PRoteomics IDEntifications (PRIDE) (https://www.ebi.ac.uk/pride/archive/) | Proteomics data repository | Stores 3342 projects on protein/peptide identifications and post-translational modifications and supporting spectral evidence |
| Additional annotation of datasets for better organization | ||
| Human Protein Atlas (http://www.proteinatlas.org/) | Protein expression and localization in different tissues and organs (immunochemistry) | Additional information regarding genes, annotations and organs Nice graphical interface |
| Metabolomics | ||
| Human Metabolome Database (http://www.hmdb.ca/) | Detailed information on metabolites (chemical, clinical and molecular biology/biochemistry levels) | Contains thousands of metabolites |
| Search in 17 different biofluids and 617 diseases | ||
| Connections with pathways, proteins and reactions | ||
| Multi-omics | ||
| Multi-Omics Profiling Expression Database (www.proteinspire.org/MOPED/) | Processed multi-omics data | Interactive visualization tools |