Skip to main content

Table 1 Overview about publicly available omic data resources

From: New perspectives: systems medicine in cardiovascular disease

Name Description URL Reference
1000 Genomesproject The goal of the 1000 genomes project was to find most genetic variants with frequencies of at least 1% in the populations studied http://www.1000genomes.org  
ArrayExpress Archive of functional genomics data stores data from high-throughput functional genomics experiments https://www.ebi.ac.uk/arrayexpress  
GEO Gene Expression Omnibus Public functional genomics data repository supporting MIAME-compliant data submissions. Tools are provided to help users query and download experiments and curated gene expression profiles http://www.ncbi.nlm.nih.gov/geo  
EBI Expression Atlas Gene expression patterns under different conditions. Data sets are re-analyzed in-house to detect baseline and differential expression patterns https://www.ebi.ac.uk/gxa [103]
GXD The Mouse Gene Expression Database Collection of gene expression data in rodents. Focus on development. http://www.informatics.jax.org/expression.shtml [104]
TCGA – The Cancer Genome Atlas Aims to assess the value of large-scale multidimensional analysis of molecular characteristics in human cancer and to provide the data rapidly to the research community. https://gdc.cancer.gov/ [53]
LINCS - The Library of Integrated Network-Based Cellular Signatures Aims to create a network-based holistic understanding of biology by cataloging changes in gene expression and other cellular processes upon perturbation. https://clue.io/ [57]
CCLE - The Cancer Cell Line Encyclopedia A compilation of gene expression, chromosomal copy number and sequencing data from 947 human cancer cell lines with pharmacological profiles for 24 anticancer drugs across 479 of the cell lines. http://www.broadinstitute.org/ccle [56]
PRIDE – PRoteomics IDEntifications Repository for proteomics data, protein and peptide identifications and post-translational modifications. https://www.ebi.ac.uk/pride/archive [105]
COPaKB Proteome biology platform specifically for cardiovascular research http://www.heartproteome.org [106]