Table 1.
Databases and tools for the identification of gene targets.
| Database/tool type | Name | Description | Website | Citation |
|---|---|---|---|---|
| eQTL | ExSNP | The ExSNP database can be used to query genetic variants and genes for associations with gene expression using 16 publicly available human eQTL studies. These data allow tissue- and population-specific eQTLs to be identified. | www.exsnp.org/ | Yu et al., 2016 |
| Blood eQTL browser | The Westra blood dataset is an eQTL meta-analysis of peripheral blood samples from ∼5,300 individuals with replication in ∼2,700 individuals. Cis- and trans-eQTLs can be queried by gene or variant. | Westra et al., 2013 | ||
| DAGS | Depression Genes and Network results of eQTL analyses for blood samples from 922 individuals are available for download. | http://dags.stanford.edu/dgn/ | Battle et al., 2014 | |
| GTEx | GTEx has matching gene expression and genotype information for >50 human tissues from >400 individuals. eQTL and splice QTL data can be queried by gene or variant. | https://gtexportal.org/home/ | Ardlie et al., 2015 | |
| Braineac | The Braineac dataset contains 134 neurodegenerative-free brains and can be queried for variants and genes associated with neurological disorders. Up to 12 brain regions were extracted per brain in parallel for mRNA quantification. Results of eQTL and genotyping analyses can be downloaded. | www.braineac.org/ | Ramasamy et al., 2014 | |
| Functional genomic | NCBI GEO | NCBI GEO database contains 4348 genomic data sets and 2,184,488 samples that are cross-linked from high-throughput microarray and next-generational sequence functional genomic data sets. It can be queried for raw, processed or meta-data. All data are also available for download. | www.ncbi.nlm.nih.gov/geo/ | Barrett et al., 2013 |
| ENCODE | ENCODE contains data from 13,393 biosamples. Queries can be made for the following experimental data: open chromatin (DNase-seq, ATAC-seq); histone mark enrichment (ChIP-seq); transcription factor binding (TF ChIP-seq); gene expression (RNA-seq); and 3D chromatin interactions (ChIA-PET). | www.encodeproject.org/ | Encode Project Consortium (2012) | |
| Roadmap Epigenomics Project | The Roadmap Epigenomics Project contains includes 1,821 histone modification datasets, 360 DNase datasets, 277 DNA methylation datasets, and 166 RNA-Seq datasets. Epigenomics data can be browsed and downloaded. | www.roadmapepigenomics.org/ | Roadmap Epigenomics Consortium et al., 2015 | |
| GWAS3D | Sets of genetic variants can be queried to identify the most probable functional variants affecting transcriptional regulation, prioritize leading variants, evaluate deleteriousness of genetic variants affecting the gene regulation and annotate genetic variants from a regulatory perspective. | http://jjwanglab.org/gwas3d | Li et al., 2013 | |
| HumanBase (NetWAS) | HumanBase is the integration of GWAS and tissue-specific networks to identify relevant disease-gene associations. It contains 144 tissue-specific functional networks and 214 biological process-specific functional networks. GWAS data files can be uploaded for analysis or HumanBase predicted tissue-specific interactions can be downloaded. | http://hb.flatironinstitute.org/ | Greene et al., 2015 | |
| EnhancerAtlas | EnhancerAtlas provides annotation of enhancers in the human genome and contains enhancers for 76 cell lines and 29 tissues. The database allows users to examine experimental evidences for predicted enhancers in a given genomic region; compare enhancers across different cell/tissue types; identify enhancers associated with a gene; predict genes regulated by a set of cis-regulatory elements. | http://enhanceratlas.org/ | Gao et al., 2016 | |
| 3D Genome Browser | 3DGenome is a platform to explore publicly available chromatin interaction data (e.g., Hi-C, ChIA-PET, Capture Hi-C, and PLAC-seq). It also provides multiple methods to link distal cis-regulatory elements with their potential target genes. | http://3dgenome.org | Wang et al., unpublished | |
| 4DGenome | 4DGenome is a repository for chromatin interaction data (i.e., 3C, 4C, 5C, ChIA-PET, and Hi-C) and bioinformatically predicted interactions (i.e., IM-PET). Records can be queried by genomic regions, gene names, organism, and detection technology. | https://4dgenome.research.chop.edu/ | Teng et al., 2015 | |
| 3DSNP | 3DSNP contains publicly available data from Hi-C experiments and can be queried by variant, gene or genomic region. | www.cbportal.org/3dsnp/index.html | Lu et al., 2017 | |
| Chromatin Chromatin Space Interaction | CCSI presents ∼3,000,000 chromatin interaction pairs with annotation of genes, enhancers and SNPs in many cell lines of human, mouse and yeast. The data was obtained by means of 3C, 4C, 5C, ChIA-PET, and Hi-C technology and can be searched by Ensembl ID, gene name, or chromatin fragment. | Xie et al., 2016 | ||
| Functional genomic tools | IM-PET | IM-PET integrates gene expression and epigenomic data to predict genes targeted by enhancers. | http://tanlab4generegulation.org/IM-PET.html | He et al., 2014 |
| PreSTIGE | PreSTIGE makes cell-specific predictions of gene/enhancer pairs by integrating H3K4Me1 histone modification and gene expression data. Publicly available data for 12 cell types can be browsed by gene or enhancer. | http://genetics.case.edu/prestige/ | Corradin et al., 2014 | |
| Genetic associations | OMIM | OMIM is an online database of >24,000 human genes and all known genetic disorders (including associated variants) that is updated daily and can be queried for clinical features, phenotypes, and genes. | www.omim.org/ | Amberger et al., 2015 |
| GWASdb | GWASdb is a database of published GWAS that can be searched by trait, variant identifier, study or gene. Catalog contains data from 3,092 publications and 53,096 unique SNP-trait associations. | www.ebi.ac.uk/gwas/ | MacArthur et al., 2017 | |
| Open Targets | Open Targets collates publicly available data to enable the identification of genes associated with disease through genetic variants and gene expression. Genes can also be queried to identify disease associations. | www.targetvalidation.org/ | Koscielny et al., 2017 | |
| Phenome Wide Association Studies | >3,000 GWAS variants were analyzed for associations with 1,358 clinical phenotypes in 13,835 European-ancestry individuals from the Electronic Medical Records and Genomics network. Data can be queried by gene, variant, or clinical phenotype. | https://phewascatalog.org/ | Denny et al., 2013 |