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. Author manuscript; available in PMC: 2024 Apr 15.
Published in final edited form as: Mol Psychiatry. 2021 Jun 30;27(1):113–126. doi: 10.1038/s41380-021-01201-2

Table 1.

Resources and tools for Omics studies.

Category Type Database/tool Short description URLs
Database Proteomics AlloMAPS Allosteric signaling and mutations in proteins http://allomaps.bii.a-star.edu.sg
Transcriptomics APAatlas Human alternative polyadenylation https://hanlab.uth.edu/apa/
Transcriptomics Coexpedia Gene co expression data mapped to medical subject headings (MeSH). http://www.coexpedia.org
Genomics/Transcriptomics GTEx A comprehensive resource for gene expression and eQTL http://www.gtexportal.org/home/
Genomics PGC GWAS summary statistics for neuropsychiatric diseases https://www.med.unc.edu/pgc/
Multi-Omics UK Biobank GWAS genotypes, Brain MRI and EMR data https://www.ukbiobank.ac.uk/
Genomics/Phenomics All of US GWAS genotypes, whole genome sequences, and EMR data https://allofus.nih.gov/
Genomics denovo-db Human de novo gene variants detected by parent-child sequencing http://denovo-db.gs.washington.edu
Genomics EnhancerAtlas Enhancers in nine species http://www.enhanceratlas.org/
Genomics Gephebase Genotype-phenotype relationships in eukaryotes www.gephebase.org
Genomics/Connectomics ENIGMA Genotypes and brain MRI data http://enigma.ini.usc.edu/
Epigenomics GIRD Gene Transcription Regulation Database http://gtrd.biouml.org
Genomics GWAS Central GWAS datasets https://www.gwascentral.org/index
Genomics Polygenic score catalog database of polygenic scores https://www.pgscatalog.org/
Epigenomics HEDD Human Enhancer Disease Database http://zdzlab.einstein.yu.edu/1/hedd.php
Genomics/Transcriptomics m6AVar Human variants affecting m6A sites http://m6avar.renlab.org/
Transcriptomics/Connectomics BrainSpan Atlas Microarray and RNA-seq expression and brain imaging data https://www.brainspan.org/static/home
Genomics/Epigenomics MGA Mass Genome Annotation http://ccg.vital-it.ch/mga/
Multi-Omics mutLBSgeneDB Mutations in Ligand Binding Sites Gene DataBase http://www.zhaobioinfo.org/mutLBSgeneDB/
Multi-Omics TSEA-DB Tissue specificity of GWAS traits and phenotypes https://bioinfo.uth.edu/TSEADB/
Transcriptomics SCPortalen Human and mouse single-cell centric database http://single-cell.clst.riken.jp/
Multi-Omics QTTbase Quantitative Trait Loci across human phenotypes http://mulinlab.org/qtlbase/index.html
Transcriptomics EVLncRNAs Experimentally Validated IncRNAs including disease indications http://biophy.dzu.edu.cn/EVLncRNAs/
Multi-Omics CommonMind Chromatin accessibility, gene expression http://commonmind.org/WP
Transcriptomics/Connectomics Brain Map Gene expression, in situ hybridization, MRI http://human.brain-map.org/
Epigenomics ReMap Transcription factor ChlP-seq data http://remap.cisreg.eu
Transcriptomics/Epigenomics spatialDB Spatially resolved transcriptome https://www.spatialomics.org/SpatialDB
Multi-Omics BrainCode Integrative analysis of the human neuronal genome, transcriptome http://www.humanbraincode.org/
Multi-Omics Allen Brain Map Multiple multi-Omics data for brain research https://portal.brain-map.org/
Transcriptomics/Cellulomics Human Cell Atlas gene expression changes in single cell https://www.humancellatlas.org/
Transcriptomics SyntDB IncRNAs and their evolutionary relationships in primates http://syntdb.amu.edu.pl/
Epigenomics mirTrans Cell-specific transcriptional information for human miRNAs http://mcube.nju.edu.cn/jwang/lab/soft/mirtrans/
Epigenomics CFEA Cell-free epigenome atlas http://www.bio-data.cn/CFEA
Genomics/Transcriptomics BrainSeq Consortium Gene expression, eQTLs http://eqtl.brainseq.org/
Epigenomics CistromeDB ChlP-Seq and DNase-Seq data in human and mouse http://cistrome.org/db
Epigenomics miRandola Extracellular and circulating noncoding RNAs http://mirandola.iit.cnr.it/
Epigenomics EWAS Data Hub DNA methylation array data and metadata https://bigd.big.ac.cn/ewas/datahub
Epigenomics 3DIV 3D-genome Interaction Viewer and database for Hi-C and pcHi-c data http://kobic.kr/3div
Multi-Omics PsychENCODE Chromatin accessibility, epigenetic modifiers, gene expression, QTLs http://psychencode.org/
Epigenomics BOCA the open chromatin by ATAC-seq assay in different brain regions and cell types http://icahn.mssm.edu/boca
Transcriptomics/Pharmacogenomics Connectivity Map Transcriptional responses to chemical, genetic, and disease perturbation https://portals.broadinstitute.org/cmap/
Transcriptomics/Proteomics Differential NET Differential protein-protein interactions in human tissues http://netbio.bgu.ac.il/diffnet
Genomics/Proteomics ActiveDriverDB Genome variation mapped against post-translational modifications https://activedriverdb.org/
Proteomics ADReCS-Target Adverse Drug Reactions linked to proteins, genes and genetic variants http://bioinf.xmu.edu.cn/ADReCS-Target
Proteomics PhaSepDB Phase separation related proteins http://db.phasep.pro/
Proteomics DisNor Protein interaction networks linking disease genes http://disnor.uniroma2.it/
Proteomics Tabloid Proteome Protein associations inferred from Mass Spectrometry http://iomics.ugent.be/tabloidproteome
Proteomics/Metabolomics pathDIP Pathway data integration and analysis portal http://ophid.utoronto.ca/pathDIP
Transcriptomics/Proteomics ProteomicsDB Mass spectrometry of the human proteome https://www.ProteomicsDB.org
Proteomics/Metabolomics Exposome-Explorer Biomarkers of exposure to disease risk factors http://exposome-explorer.iarc.fr
Genomics ExAC browser Exome Aggregation Consortium sequence data http://exac.broadinstitute.org
Genomics PopHuman Population genomics-oriented genome browser http://pophuman.uab.cat
Proteomics Membranome A database of single-pass membrane proteins http://membranome.org/
Proteomics KEGG integrated database to understand high-level functions http://www.genome.ad.jp/kegg/
Metabolomics METLIN A metabolite mass spectral database https://metlin.scripps.edu
Metabolomics HMDB Human metabolome database http://www.hmdb.ca
Multi-Omics jMorp Multi-Omics dataset of 1000 healthy Japanese people https://jmorp.megabank.tohoku.ac.jp/
Metabolomics LIPID MAPS in depth knowledge of lipid structure and function http://www.lipidmaps.org/
Microbiomics gutMEGA Human gut metagenomics data http://gutmega.omicsbio.info/
Microbiomics gutMDisorder Dysbiosis of the gut microbiota http://bio-annotation.cn/gutMDisorder
Connectomics Human Connectome Project Multimodal imaging data across the lifespan https://www.humanconnectome.org/
Tools Genomics/Phenomics MRBase Mendelian randomization using summary data from genome-wide association studies http://www.mrbase.org
Genomics CausalDB Predicted causal variants from GWAS http://mulinlab.org/causaldb
Genomics/Epigenomics FATHMM prediction of pathogenic point mutations http://fathmm.biocompute.org.uk
Genomics/Epigenomics Fgwas a command line tool for integrating functional genomic information into a genome-wide association study https://github.com/joepickrell/fgwas
Genomics/Transcriptomics TWAS Imputed gene expression and perform TWAS https://github.com/hakyimlab/PrediXcan
Multi-Omics PINSPIus Omics data integration and disease subtyping https://cran.r-project.org/web/packages/PINSPIus/
Genomics/Epigenomics GARFIELD a functional enrichment analysis approach described the GWAS analysis https://www.ebi.ac.uk/birney-srv/GARFIELD/
Transcriptomics WGCNA Weighted gene co expression network analysis to build gene modules https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/RpackagesWGCNA/
Multi-Omics ENLOC integrative genetic association analysis of molecular QTL data and GWAS data https://github.com/xqwen/integrative
Genomics/Transcriptomics eCaviar Co-localization of eQTLs and trait-associated loci https://github.com/fhormoz/caviar
Genomics/Transcriptomics/ Epigenomics SLDP a method for looking for a directional effect of a signed functional annotation on a heritable trait using GWAS summary statistics. https://github.com/yakirr/sldp
Multi-Omics Integrated systems genetics toolkit Annotate gene function using multi-omics datasets https://www.systems-genetics.org/
Genomics/Epigenomics PAINTOR Enrichment analysis of global trait-associated variants within annotations https://github.com/gkichaev/PAINTOR_V3.0
Genomics/Epigenomics GoShifter a method to determine enrichment of annotations in GWAS significant loci. https://github.com/immunogenomics/goshifter
Genomics PRSice Calculate and apply polygenic risk scores analyses https://www.prsice.info/
Genomics/Transcriptomics PrediXcan an approach to estimate the genetic association between disease risk and the local gene expression of thousands of genes. http://twas-hub.org
Genomics/Transcriptomics SMR Test for pleiotropic association between gene expression and complex trait https://cnsgenomics.com/software/smr/
Multi-Omics PsychENCODE-DSPN Integrative omic analysis by deep learning https://github.com/gersteinlab/PsychENCODE-DSPN
Genomics/Transcriptomics MESC Estimate complex trait heritability mediated by assayed gene expression levels https://github.com/douglasyao/mesc
Transcriptomics SCRNA-tools designed for analyzing scRNA-seq data https://www.scrna-tools.org/
Connectomics nilearn machine learning for neuroimaging in python https://github.com/nilearn/nilearn
Transcriptomics Networknalyst comprehensive gene expression analysis, meta-analysis & network biology https://www.networkanalyst.ca/
Genomics/Epigenomics PleioPred a framework that leverages pleiotropy and functional annotations in genetic risk prediction https://github.com/yiminghu/PleioPred
Epigenomics MethSurv perform multivariable survival analysis using DNA methylation data https://biit.cs.ut.ee/methsurv/
Genomics/Epigenomics GREGOR a tool built to evaluate global enrichment of trait-associated variants in experimentally annotated epigenomic regulatory features. https://genome.sph.umich.edu/wiki/GREGOR
Epigenomics eFORGE Histone labeling https://eforge.altiusinstitute.org
Proteomics IMP functional context of gene-gene networks http://imp.princeton.edu/
Microbiomics MetaNetX Automated Model Construction and Genome Annotation for Large-Scale Metabolic Networks https://www.metanetx.org/
Microbiomics microbiomeDB Mining and analyzing microbiome data http://microbiomeDB.org

Database and tools handling ≥3 types of omics data are denoted as ‘Multi-Omics’.