The IntAct molecular interaction database in 2012

Abstract

IntAct is an open-source, open data molecular interaction database populated by data either curated from the literature or from direct data depositions. Two levels of curation are now available within the database, with both IMEx-level annotation and less detailed MIMIx-compatible entries currently supported. As from September 2011, IntAct contains approximately 275 000 curated binary interaction evidences from over 5000 publications. The IntAct website has been improved to enhance the search process and in particular the graphical display of the results. New data download formats are also available, which will facilitate the inclusion of IntAct's data in the Semantic Web. IntAct is an active contributor to the IMEx consortium (http://www.imexconsortium.org). IntAct source code and data are freely available at http://www.ebi.ac.uk/intact.

Methods for protein complex prediction and their contributions towards understanding the organisation, function and dynamics of complexes

“…We obtain PPI data by combining physical interactions from the BioGRID [27], IntAct [63,64] and MINT [75] repositories. These repositories catalogue interactions detected from a multitude of studies, e.g.…”

Integrative methods for analyzing big data in precision medicine

“…Link Content NCBI Gene [66] www.ncbi.nlm.nih.gov/gene Atlas of 59,500 human genes GOA [67] www.ebi.ac.uk/GOA 487,409 Gene Ontology annotations for 48,569 human gene products ENCODE [68] www.encodeproject.org Functional annotations of coding/non-coding DNA elements NCBI Epigenomics [69] www.ncbi.nlm.nih.gov/epigenomics 5,110 epigenetic modifications 4DGenome [70] 4dgenome [73] www.ebi.ac.uk/gxa Differential and baseline gene expression data CMAP [74] www.broadinstitute.org/cmap ∼ 7,000 expression profiles for 1,309 perturbagen compounds COXPRESdb [75] coxpresdb.jp Co-expression of 19,803 human genes GeneFriends [76] genefriends.org Co-expression of 159,184 human genes and transcripts UniProt [77] www.uniprot.org Information about human proteome (69,693 proteins) NeXtProt [78] www.nextprot.org Knowledgebase on 20,066 human proteins RCSB PDB [79] www.rcsb.org/pdb Portal to 113,494 biological macromolecular 3D-structures HPA [80] www.thehpp.org Maps of human proteome on 44 normal and 20 cancer type tissues IntAct [81] www.ebi.ac.uk/intact 209,852 human protein-protein interactions BioGrid [82] thebiogrid.org 215,952 human protein-protein interactions I2D [83] ophid.utoronto.ca 183,524 (+ 55,985 predicted) protein-protein interactions STRING [84] string-db.org 8,548,005 interactions between 20,457 proteins HMDB [85] www.hmdb.ca Atlas of 41,993 human metabolites KEGG Pathway [86] www.genome.jp/kegg/pathway 298 human pathways SMPD [87] www.smpdb.ca ∼700 human metabolic and disease pathways Reactome [88] www.reactome.org 8,770 reactions in 1,887 human pathways SugarBindDB [89] sugarbind.expasy.org 1,256 interactions between 200 glycans and 551 pathogenic agents UniCarbKB [90] www.unicarbkb.org 3,740 glycan structure entries and 400 glycoproteins KEGG Glycan [91] www.genome.jp/kegg/glycan/ Glycan metabolic pathways OMIM [92] www.omim.org Catalog of mendelian disorders and over 15,000 genes NCBI dbGaP [93] www.ncbi.nlm.nih.gov/gap Database of genotypes and phenotypes GWAS Catalog [94] www.ebi.ac.uk/gwas/ Genome wide association studies, assaying ∼ 100,000 SNPs COSMIC...…”

Identification of Key Proteins Associated with Myocardial Infarction using Bioinformatics and Systems Biology

“…Interactions from 5 databases were imported and merged for constructing the PPI network-iRefIndex (Razick, Magklaras and Donaldson, 2008), APID Interactomes (Alonso- López et al, 2016), menthe (Calderone, Castagnoli and Cesareni, 2013), IntAct (Kerrien et al, 2012), InnateDB-all (Breuer et al, 2013). From the initial network, connected components were identified and the largest individual connected component was extracted to generate a separate second network.…”