Chemogenomics: Bioinformatic software and tools

BioGRID ORCS provides a unified repository for all published CRISPR screen data. A user-friendly interface allows for searching, filtering and downloading of CRISPR screen datasets. ORCS displays results at the publication-, screen- and gene-level with original scores and significance thresholds, along with information about associated analytical methods and other metadata when available. Current screen formats in ORCS include negative and positive selection screens based on viability and other phenotypic readouts in conjunction with nuclease-mediated knockout (CRISPRn), transcriptional activation (CRISPRa) and transcriptional inactivation (CRISPRi) library designs.

The Biological General Repository for nteraction Datasets (BioGRID: https://thebiogrid.org) is an open access database dedicated to the curation and archival storage of protein, genetic and chemical interactions for all major model organism species and humans. All data in BioGRID is made freely available without restriction, is directly downloadable in standard formats and can be readily incorporated into existing applications via our web service platforms. BioGRID data are also freely distributed through partner model organism databases and meta-databases.

GIX is a browser extension that allows the efficient retrieval of information about genes and gene products from within any open webpage. GIX can be run with either Google Chrome or Mozilla Firefox and can be customized by users to retrieive information on gene function, gene expression, protein interactions, protein localization, Gene Ontology terms, and disease associations. Information for any gene from humans or major model organism species can be retrieved by simply double clicking on the gene name in an open browser window. GIX enables rapid interrogation of gene function from any online format. See Knight et al (2019).