This repository contains lists of genes with particular phenotypic associations. It is based on the Macarthur lab's resource, but has been updated and to focus on GPCR genes.
| List | Count | Description | Please cite |
|---|---|---|---|
| Universe | 19,208 | Approved symbols for 19,208 protein-coding genes. This list is the "universe" of which all subsequent lists are subsets. | "HUGO Gene Nomenclature Committee at the European Bioinformatics Institute" (http://www.genenames.org/) |
| GPCR genes by family | 392+ | Non-olfactory protein-coding GPCR genes from GuideToPharmacology with families from GPCRdb | [UniProt Consortium 2018] [Alexander 2017 & Harding 2018] |
| Approved or investigational drug targets | 385 | Genes whose protein products are known to be the mechanistic targets of FDA-approved drugs (updated 2018-09-13). For details on the exact criteria we used for inclusion in this list, see src/drug_targets.py | See drugbank.ca/about. Please cite [Law 2014, Knox 2011, Wishart 2008, Wishart 2006, and/or Wishart 2018]. |
| Genetic disease genes | 2000+ | Data from OMIM and with additional curation from the union of the Berg and Blekhman dominant & recessive lists | [Blekhman 2008, Berg 2013] [Rehm 2015] |
| Essential in mice | 2,454 | Genes where homozygous knockout in mice results in pre-, peri- or post-natal lethality. The mouse phenotypes were reported by Jackson Labs [Blake 2011], then essential gene list was extracted via manual review of phenotypes by [Georgi 2013], and the essential/non-essential flag was put into dbNSFP [Liu 2013]. We extracted the genes from dbNSFP. Also need to add IMPC if this is different? | [Blake 2011, Georgi 2013, and Liu 2013] |
| Essential in human cells | 2,454 | Genes where homozygous knockout in mice results in pre-, peri- or post-natal lethality. The mouse phenotypes were reported by Jackson Labs [Blake 2011], then essential gene list was extracted via manual review of phenotypes by [Georgi 2013], and the essential/non-essential flag was put into dbNSFP [Liu 2013]. We extracted the genes from dbNSFP. Also need to add IMPC if this is different? | [Blake 2011, Georgi 2013, and Liu 2013] |
- Human GPCR genes were extracted from Guide To Pharmacology and annotated with GPCRdb family slugs
- GPCR-linked genetic disease were extracted from the work of Schoeneberg (2021) and modes of inheritance were assigned based on OMIM data
- GPCR drug targets were extracted from drugbank
- GPCRs with associated mouse phenotypes were extracted from IMPC data
- Drug targets from [Nelson 2012, Russ & Lampel 2005]
- Add Olfactory receptors from Mainland 2015's data release; Kinases; Nuclear receptors [Hunter 2000, Manning 2002, Miranda-Saavedra & Barton 2007]
- Also possibly include Natural product targets from [Dancik 2010]
- Genes deemed essential in multiple cultured cell lines based on shRNA and CRISPR/Cas screening data [Hart 2014, Hart 2017]
- add ClinVar [Landrum 2014] later & Genes with sufficient evidence for dosage pathogenicity (level 3) as determined by the ClinGen Dosage Sensitivity Map as of Sep 13, 2018
The files required are
drugbank.xml- this contains the whole DrugBank database in XML form and can be downloaded from the drugbank websiteopentargets_drugs_20.06.json- this contains all opentargets evidence relating to drugs. it can be downloaded fromftp.ebi.ac.uk/pub/databases/opentargets/platform/21.11/output/etl/json/moleculeATC.csv- this contains definitions for all WHO ATC codes. It can be downloaded fromhttps://bioportal.bioontology.org/ontologies/ATC/guidetopharm_drugs.csv- this contains all approved drugs in the GuideToPharmacology database and their primary targets. It can be downloaded fromhttps://www.guidetopharmacology.org/DATA/approved_drug_primary_target_interactions.csvguidetopharm_targets.csv- this contains all targets in the GuideToPharmacology database, annotated with families. It can be downloaded fromhttps://www.guidetopharmacology.org/DATA/targets_and_families.csv