Table 1 |.
Systems genetics resources
| Category | Name | Description |
|---|---|---|
| Population-based resources | BXD genetic reference panel | Diverse mouse panel derived from intercrosses of C57BL6J and DBA strains; http://www.genenetwork.org/mouseCross.html |
| HMDP | Collection of ~100 classical and recombinant inbred strains; https://systems.genetics.ucla.edu/ | |
| Attie Lab Diabetes Database | Several mouse crosses, molecular layers and phenotypes associated with diabetes development; http://diabetes.wisc.edu/ | |
| DO panel | Outbred population of mice derived from eight founder strains; http://churchill-lab.jax.org/website/ | |
| GTEx Portal | Collection of WGS, WES and RNA-sequencing data from multiple post-mortem tissues of ~1,000 people; https://www.gtexportal.org/home/index.html | |
| STARNET | Collection of genomic, multi-tissue transcriptomic and proteomic data from ~1,300 patients with, and 300 verified controls without, coronary artery disease; https://doi.org/10.1126/science.aad6970 | |
| METSIM | Longitudinal study in ~10,000 Finnish men, for whom genomic, transcriptomic (subcutaneous adipose tissue) and comprehensive metabolic phenotypes are available; https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000743.v1.p1 | |
| TwinsUK | Collection of phenotypic, genomic, environmental and several intermediate molecular phenotype samples from ~1,200 sibling pairs in the United Kingdom; https://twinsuk.ac.uk/ | |
| UK Biobank | Large collection of genotypic, health and disease parameters from ~500,000 people; https://www.ukbiobank.ac.uk/ | |
| MUTHER (Multiple Tissue Human Expression Resource) | Collection of multi-tissue expression profiles and genomic data from ~850 UK twins; http://muther.ac.uk/ | |
| Statistical/modelling resources | Mergeomics | Integrative analysis to merge multiscale data at the pathway level and identify network key drivers; http://mergeomics.research.idre.ucla.edu/ |
| WGCNA | Network construction to generate coregulated modules and overlay with other data (for example, networks of genes to traits); https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/ | |
| MEGENA | Network construction to generate coregulated modules; https://doi.org/10.1371/journal.pcbi.1004574 | |
| MOFA | Approach to infer relationships between scales exclusively by using quantitative measures; https://github.com/bioFAM/MOFA | |
| ARACNE | Approach to generate co-expression networks, focused on eliminating indirect interactions; https://doi.org/10.1186/1471–2105-7-S1-S7 | |
| Pathway-analysis Resources | NURSA (Nuclear Receptor Signaling Atlas) | Collection of published data related to nuclear-receptor function and specific pathways; https://nursa.org/nursa/index.jsf |
| GO enrichment analysis | Deposited sets of functional annotations for gene and proteins; http://geneontology.org/ | |
| KEGG | Deposited sets of cellular annotations for genes, including localization and function; https://www.genome.jp/kegg/ | |
| IPA (Ingenuity Pathway Analysis) | Comprehensive pathway-annotation software; https://www.qiagenbioinformatics.com/products/ingenuity-pathway-analysis/ | |
| Reactome | Interaction database to query genes or proteins; https://reactome.org/ | |
| BRENDA | Database of enzymatic pathways, including structure and kinetics; https://brenda-enzymes.org/ | |
| Additional Resources | BioGPS | Expression profiles from many tissues and cell lines from mouse or human data; http://biogps.org/#goto=welcome |
| Systems-Genetics.org | Systems Genetics toolkits to assess gene function and trait relationships. https://systems-genetics.org/ | |
| Gene Networks | Database to investigate gene functions and/or trait relationships; http://gn2.genenetwork.org/ | |
| UniProt | Collection of published terms (for example, pathways and localization) for individual genes and proteins across many organisms; https://www.uniprot.org/ | |
| Human Protein Atlas | Combined proteomic, transcriptional and cellular localization data across human tissues and cell types; http://proteinatlas.org/ | |
| HMDB (The Human Metabolome Database) | Collection of deposited data from human metabolomics studies; http://hmdb.ca/ | |
| CMAP | Compound prediction using gene expression data; http://clue.io/cmap/ | |
| MGI (Mouse Genome Informatics) | Integrated database for laboratory mouse strains and lines; http://informatics.jax.org/ | |
| IMPC (International Mouse Phenotyping Consortium) | Curated database of pheonotyping outcomes from mouse knockout lines for 20,000 genes; http://mousephenotype.org/ | |
| PredictDB Repository | Database of imputation tools to investigate molecular layers contributing to GWAS results; http://predictdb.hakyimlab.org/ | |
| STRING (search tool for recurring instances of neighbouring genes) | Collection of protein-protein interactions from published studies; http://string-db.org/ | |
| BioGRID (Biological General Repository for Interaction Datasets) | Interaction database to query genes or proteins; http://thebiogrid.org/ | |