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. Author manuscript; available in PMC: 2021 Jun 5.
Published in final edited form as: Circ Res. 2020 Jun 4;126(12):1795–1815. doi: 10.1161/CIRCRESAHA.119.315863

Table 3. Representative resources for Systems Genetics studies.

Type Resource Name G E T Pr Me Mi Ph Q I Description Website
Repository Array Express X X X X Large repository of systems genetics data across multiple layers http://www.ebi.ac.uk/arrayexpress/
Repository BioGrid X X X Interaction data from genetic and proteomic studies https://thebiogrid.org/
Repository Database of Interacting Proteins X X Large repository of protein-protein interactions https://dip.doe-mbi.ucla.edu/dip/Main.cgi
Repository dbGaP X X X Large repository for raw GWAS data for human studies https://www.ncbi.nlm.nih.gov/gap/
Repository EBI GWAS Catalog X Large repository of published GWAS studies in humans https://www.ebi.ac.uk/gwas/
Repository Encode Project X X Repository of information on epigenetic marks https://www.encodeproject.org/
Repository Epigenomics Roadmap Project X X Human epigenomic information in multiple tissues and diseases http://www.roadmapepigenomics.org/
Repository European Genome-Phenome Archive X X X X X Repository of human systems genetics data https://ega-archive.org/
Repository Framingham Heart Study X X X X A cardiovascular disease study active since 1948 https://www.framinghamheartstudy.org/
Repository GEO X X X X Large repository for multiple biological layers, but mostly pertaining to the transcriptome https://www.ncbi.nlm.nih.gov/geo/
Repository GWAS Central X Repository for genetic association studies https://gwascentral.org
Repository Harvard Personal Genome Project X X X Multi-layer data from volunteers https://pgp.med.harvard.edu/
Repository Human Metabolome Database X Repository for metabolites in disease and healthy states http://www.hmdb.ca/
Repository IntAct Database X X Large repository of protein-protein interactions https://www.ebi.ac.uk/intact/
Repository Japanese Genotype-Phenotype Archive X X X Repository of human systems genetics data from Japan https://www.ddbj.nig.ac.jp/jga/index-e.html
Repository Metabolic Syndrome in Men Study (Metsim) X X X X X X A comprehensive systems genetics study for metabolic syndrome and related disorders https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000743.v1.p1
Repository MetaboLights X Large metabolite repository https://www.ebi.ac.uk/metabolights/
Repository MicrobiomeDB X Repository for microbiome data from multiple species https://microbiomedb.org/mbio/app/
Repository Pride Archive X A proteomics data repository from EBI https://www.ebi.ac.uk/pride/archive/
Repository SRA X X X X A large repository of sequence data from multiple layers https://www.ncbi.nlm.nih.gov/sra
Repository Twin UK X X X X X Large twin registry with over 14,000 individuals https://twinsuk.ac.uk
Repository UK Biobank X X X X National health resource following 500,000 individuals https://www.ukbiobank.ac.uk/
Data Curator Collaborative Cross Resource X X A mouse systems genetics resource http://csbio.unc.edu/CCstatus/index.py
Data Curator GeneWeaver X X Aggregator of transcriptome data and positional candidate genes for many species and phenotypes of interest https://geneweaver.org
Data Curator GTEx X X X X Large repository for tissue expression across 54 tissues and over 1000 individuals https://gtexportal.org/home/
Data Curator HMDP Liver EWAS Database X X X X X X X A comprehensive systems genetics resource focused on EWAS results from the liver in the HMDP http://ewas.mcdb.ucla.edu/
Data Curator MassIVE X A repository and analysis tool for mass spectrometry data https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp
Data Curator Mouse Genome Informatics X X X X Large database for mouse systems genetics data http://www.informatics.jax.org/
Data Curator NIH Human Microbiome Project X Microbiome data from multiple individuals https://hmpdacc.org/
Data Curator Omics Discovery Index X X X X X Aggregator for many layers of systems genetics data https://www.omicsdi.org/
Data Curator Rat Genome Database X X X X Large database for rat systems genetics data https://rgd.mcw.edu/
Data Curator UCLA Systems Genetics Resource X X X X Database containing information from the HMDP systems genetics resource as well as some human data https://systems.genetics.ucla.edu/
Links Curated Multi-omics Algorithms X X X X X X X X Continually updated list of current Multi-omics algorithms https://github.com/mikelove/awesome-multi-omics
Links Curated Single Cell Algorithms X X X Continually updated list of current single cell algorithms https://github.com/seandavi/awesome-single-cell
Links Epigenie Epigenomics Links X Very large list of useful epigenomics links https://epigenie.com/epigenetic-tools-and-databases/
Links Metabolomics Society Links X Links on metabolomics http://metabolomicssociety.org/resources/metabolomics-databases
Links Metabolomix EWAS Links X X X Links to EWAS studies http://www.metabolomix.com/a-table-of-all-published-ewas-with-deep-molecular-phenotypes-omics/
Links Metabolomix glycomics QTL Links X X X X Links to glycomics QTL studies http://www.metabolomix.com/a-table-of-all-published-gwas-with-glycomics/
Links Metabolomix meQTL Links X X X X Links to meQTL studies http://www.metabolomix.com/a-table-of-all-published-gwas-with-dna-methylation/
Links Metabolomix mQTL Links X X X X Links to mQTL studies http://www.metabolomix.com/list-of-all-published-gwas-with-metabolomics/
Links Metabolomix pQTL Links X X X X Links to pQTL studies http://www.metabolomix.com/a-table-of-all-published-gwas-with-proteomics/

G, Genome; E, Epigenome; T, Transcriptome; Pr, Proteome; Me, Methylation; Mi, Microbiome; Ph, Phenome; Q, Quantitative Traits; I, Interactome.