Cargando…
IID 2018 update: context-specific physical protein–protein interactions in human, model organisms and domesticated species
Knowing the set of physical protein–protein interactions (PPIs) that occur in a particular context—a tissue, disease, or other condition—can provide valuable insights into key research questions. However, while the number of identified human PPIs is expanding rapidly, context information remains lim...
Autores principales: | , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2019
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323934/ https://www.ncbi.nlm.nih.gov/pubmed/30407591 http://dx.doi.org/10.1093/nar/gky1037 |
_version_ | 1783385873216176128 |
---|---|
author | Kotlyar, Max Pastrello, Chiara Malik, Zara Jurisica, Igor |
author_facet | Kotlyar, Max Pastrello, Chiara Malik, Zara Jurisica, Igor |
author_sort | Kotlyar, Max |
collection | PubMed |
description | Knowing the set of physical protein–protein interactions (PPIs) that occur in a particular context—a tissue, disease, or other condition—can provide valuable insights into key research questions. However, while the number of identified human PPIs is expanding rapidly, context information remains limited, and for most non-human species context-specific networks are completely unavailable. The Integrated Interactions Database (IID) provides one of the most comprehensive sets of context-specific human PPI networks, including networks for 133 tissues, 91 disease conditions, and many other contexts. Importantly, it also provides context-specific networks for 17 non-human species including model organisms and domesticated animals. These species are vitally important for drug discovery and agriculture. IID integrates interactions from multiple databases and datasets. It comprises over 4.8 million PPIs annotated with several types of context: tissues, subcellular localizations, diseases, and druggability information (the latter three are new annotations not available in the previous version). This update increases the number of species from 6 to 18, the number of PPIs from ∼1.5 million to ∼4.8 million, and the number of tissues from 30 to 133. IID also now supports topology and enrichment analyses of returned networks. IID is available at http://ophid.utoronto.ca/iid. |
format | Online Article Text |
id | pubmed-6323934 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-63239342019-01-10 IID 2018 update: context-specific physical protein–protein interactions in human, model organisms and domesticated species Kotlyar, Max Pastrello, Chiara Malik, Zara Jurisica, Igor Nucleic Acids Res Database Issue Knowing the set of physical protein–protein interactions (PPIs) that occur in a particular context—a tissue, disease, or other condition—can provide valuable insights into key research questions. However, while the number of identified human PPIs is expanding rapidly, context information remains limited, and for most non-human species context-specific networks are completely unavailable. The Integrated Interactions Database (IID) provides one of the most comprehensive sets of context-specific human PPI networks, including networks for 133 tissues, 91 disease conditions, and many other contexts. Importantly, it also provides context-specific networks for 17 non-human species including model organisms and domesticated animals. These species are vitally important for drug discovery and agriculture. IID integrates interactions from multiple databases and datasets. It comprises over 4.8 million PPIs annotated with several types of context: tissues, subcellular localizations, diseases, and druggability information (the latter three are new annotations not available in the previous version). This update increases the number of species from 6 to 18, the number of PPIs from ∼1.5 million to ∼4.8 million, and the number of tissues from 30 to 133. IID also now supports topology and enrichment analyses of returned networks. IID is available at http://ophid.utoronto.ca/iid. Oxford University Press 2019-01-08 2018-11-08 /pmc/articles/PMC6323934/ /pubmed/30407591 http://dx.doi.org/10.1093/nar/gky1037 Text en © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Database Issue Kotlyar, Max Pastrello, Chiara Malik, Zara Jurisica, Igor IID 2018 update: context-specific physical protein–protein interactions in human, model organisms and domesticated species |
title | IID 2018 update: context-specific physical protein–protein interactions in human, model organisms and domesticated species |
title_full | IID 2018 update: context-specific physical protein–protein interactions in human, model organisms and domesticated species |
title_fullStr | IID 2018 update: context-specific physical protein–protein interactions in human, model organisms and domesticated species |
title_full_unstemmed | IID 2018 update: context-specific physical protein–protein interactions in human, model organisms and domesticated species |
title_short | IID 2018 update: context-specific physical protein–protein interactions in human, model organisms and domesticated species |
title_sort | iid 2018 update: context-specific physical protein–protein interactions in human, model organisms and domesticated species |
topic | Database Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323934/ https://www.ncbi.nlm.nih.gov/pubmed/30407591 http://dx.doi.org/10.1093/nar/gky1037 |
work_keys_str_mv | AT kotlyarmax iid2018updatecontextspecificphysicalproteinproteininteractionsinhumanmodelorganismsanddomesticatedspecies AT pastrellochiara iid2018updatecontextspecificphysicalproteinproteininteractionsinhumanmodelorganismsanddomesticatedspecies AT malikzara iid2018updatecontextspecificphysicalproteinproteininteractionsinhumanmodelorganismsanddomesticatedspecies AT jurisicaigor iid2018updatecontextspecificphysicalproteinproteininteractionsinhumanmodelorganismsanddomesticatedspecies |