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’.