The BioGRID interaction database: 2015 update

Abstract

The Biological General Repository for Interaction Datasets (BioGRID: http://thebiogrid.org) is an open access database that houses genetic and protein interactions curated from the primary biomedical literature for all major model organism species and humans. As of September 2014, the BioGRID contains 749 912 interactions as drawn from 43 149 publications that represent 30 model organisms. This interaction count represents a 50% increase compared to our previous 2013 BioGRID update. BioGRID data are freely distributed through partner model organism databases and meta-databases and are directly downloadable in a variety of formats. In addition to general curation of the published literature for the major model species, BioGRID undertakes themed curation projects in areas of particular relevance for biomedical sciences, such as the ubiquitin-proteasome system and various human disease-associated interaction networks. BioGRID curation is coordinated through an Interaction Management System (IMS) that facilitates the compilation interaction records through structured evidence codes, phenotype ontologies, and gene annotation. The BioGRID architecture has been improved in order to support a broader range of interaction and post-translational modification types, to allow the representation of more complex multi-gene/protein interactions, to account for cellular phenotypes through structured ontologies, to expedite curation through semi-automated text-mining approaches, and to enhance curation quality control.

Exposure to the widely used herbicide atrazine results in deregulation of global tissue-specific RNA transcription in the third generation and is associated with a global decrease of histone trimethylation in mice

“…To evaluate this hypothesis, we asked whether DEGs we identified are targets of POU5F1. We performed the comparative analysis of DEGs and Pou5f1 targets using BioGRID (BioGRID Version 3.4.139) (114) and published dataset (115). We identified 18 Pou5f1 target genes that are altered in ATZ lineage SG (Supplementary Figure S12B).…”

Stability of a giant connected component in a complex network

“…The second is the network of human protein-protein interactions (PPI) that we derived from the BioGRID database [26]. We represent the PPI dataset as a twolayer interdependent network, where layer A is formed by direct protein interactions, and links in layer B corre-Appendix B: GCC stability of single layer networks close to the criticality…”

NF‐Y‐dependent regulation of glutamate receptor 4 expression and cell survival in cells of the oligodendrocyte lineage

“…To derive an interactome model for AMPA/CTZ and Garcinol treated cells, differentially expressed genes were used as “seeds” and all known protein/protein interactions between the seeds and their inferred immediate neighbors were identified to generate a biological network using the BioGRID model of the human Interactome (3.4.145; Chatr‐Aryamontri et al, 2015). Network generation and processing was performed using Cytoscape 2.8.3 (Smoot, Ono, Ruscheinski, Wang, & Ideker, 2011).…”