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Integrated interactions database: tissue-specific view of the human and model organism interactomes
IID (Integrated Interactions Database) is the first database providing tissue-specific protein–protein interactions (PPIs) for model organisms and human. IID covers six species (S. cerevisiae (yeast), C. elegans (worm), D. melonogaster (fly), R. norvegicus (rat), M. musculus (mouse) and H. sapiens (...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702811/ https://www.ncbi.nlm.nih.gov/pubmed/26516188 http://dx.doi.org/10.1093/nar/gkv1115 |
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author | Kotlyar, Max Pastrello, Chiara Sheahan, Nicholas Jurisica, Igor |
author_facet | Kotlyar, Max Pastrello, Chiara Sheahan, Nicholas Jurisica, Igor |
author_sort | Kotlyar, Max |
collection | PubMed |
description | IID (Integrated Interactions Database) is the first database providing tissue-specific protein–protein interactions (PPIs) for model organisms and human. IID covers six species (S. cerevisiae (yeast), C. elegans (worm), D. melonogaster (fly), R. norvegicus (rat), M. musculus (mouse) and H. sapiens (human)) and up to 30 tissues per species. Users query IID by providing a set of proteins or PPIs from any of these organisms, and specifying species and tissues where IID should search for interactions. If query proteins are not from the selected species, IID enables searches across species and tissues automatically by using their orthologs; for example, retrieving interactions in a given tissue, conserved in human and mouse. Interaction data in IID comprises three types of PPI networks: experimentally detected PPIs from major databases, orthologous PPIs and high-confidence computationally predicted PPIs. Interactions are assigned to tissues where their proteins pairs or encoding genes are expressed. IID is a major replacement of the I2D interaction database, with larger PPI networks (a total of 1,566,043 PPIs among 68,831 proteins), tissue annotations for interactions, and new query, analysis and data visualization capabilities. IID is available at http://ophid.utoronto.ca/iid. |
format | Online Article Text |
id | pubmed-4702811 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-47028112016-01-07 Integrated interactions database: tissue-specific view of the human and model organism interactomes Kotlyar, Max Pastrello, Chiara Sheahan, Nicholas Jurisica, Igor Nucleic Acids Res Database Issue IID (Integrated Interactions Database) is the first database providing tissue-specific protein–protein interactions (PPIs) for model organisms and human. IID covers six species (S. cerevisiae (yeast), C. elegans (worm), D. melonogaster (fly), R. norvegicus (rat), M. musculus (mouse) and H. sapiens (human)) and up to 30 tissues per species. Users query IID by providing a set of proteins or PPIs from any of these organisms, and specifying species and tissues where IID should search for interactions. If query proteins are not from the selected species, IID enables searches across species and tissues automatically by using their orthologs; for example, retrieving interactions in a given tissue, conserved in human and mouse. Interaction data in IID comprises three types of PPI networks: experimentally detected PPIs from major databases, orthologous PPIs and high-confidence computationally predicted PPIs. Interactions are assigned to tissues where their proteins pairs or encoding genes are expressed. IID is a major replacement of the I2D interaction database, with larger PPI networks (a total of 1,566,043 PPIs among 68,831 proteins), tissue annotations for interactions, and new query, analysis and data visualization capabilities. IID is available at http://ophid.utoronto.ca/iid. Oxford University Press 2016-01-04 2015-10-29 /pmc/articles/PMC4702811/ /pubmed/26516188 http://dx.doi.org/10.1093/nar/gkv1115 Text en © The Author(s) 2015. 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 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 Sheahan, Nicholas Jurisica, Igor Integrated interactions database: tissue-specific view of the human and model organism interactomes |
title | Integrated interactions database: tissue-specific view of the human and model organism interactomes |
title_full | Integrated interactions database: tissue-specific view of the human and model organism interactomes |
title_fullStr | Integrated interactions database: tissue-specific view of the human and model organism interactomes |
title_full_unstemmed | Integrated interactions database: tissue-specific view of the human and model organism interactomes |
title_short | Integrated interactions database: tissue-specific view of the human and model organism interactomes |
title_sort | integrated interactions database: tissue-specific view of the human and model organism interactomes |
topic | Database Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702811/ https://www.ncbi.nlm.nih.gov/pubmed/26516188 http://dx.doi.org/10.1093/nar/gkv1115 |
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