OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms

Motivation: Protein interaction networks contain a wealth of biological information, but their large size often hinders cross-organism comparisons. We present OrthoNets, a Cytoscape plugin that displays protein–protein interaction (PPI) networks from two organisms simultaneously, highlighting orthol...

Descripción completa

Detalles Bibliográficos
Autores principales: Hao, Yanqi, Merkoulovitch, Anna, Vlasblom, James, Pu, Shuye, Turinsky, Andrei L., Roudeva, Denitza, Turner, Brian, Greenblatt, Jack, Wodak, Shoshana J.
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2011
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3051336/
https://www.ncbi.nlm.nih.gov/pubmed/21257609
http://dx.doi.org/10.1093/bioinformatics/btr035
_version_ 1782199473041047552
author Hao, Yanqi
Merkoulovitch, Anna
Vlasblom, James
Pu, Shuye
Turinsky, Andrei L.
Roudeva, Denitza
Turner, Brian
Greenblatt, Jack
Wodak, Shoshana J.
author_facet Hao, Yanqi
Merkoulovitch, Anna
Vlasblom, James
Pu, Shuye
Turinsky, Andrei L.
Roudeva, Denitza
Turner, Brian
Greenblatt, Jack
Wodak, Shoshana J.
author_sort Hao, Yanqi
collection PubMed
description Motivation: Protein interaction networks contain a wealth of biological information, but their large size often hinders cross-organism comparisons. We present OrthoNets, a Cytoscape plugin that displays protein–protein interaction (PPI) networks from two organisms simultaneously, highlighting orthology relationships and aggregating several types of biomedical annotations. OrthoNets also allows PPI networks derived from experiments to be overlaid on networks extracted from public databases, supporting the identification and verification of new interactors. Any newly identified PPIs can be validated by checking whether their orthologs interact in another organism. Availability: OrthoNets is freely available at http://wodaklab.org/orthonets/. Contact: jim.vlasblom@utoronto.ca
format Text
id pubmed-3051336
institution National Center for Biotechnology Information
language English
publishDate 2011
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-30513362011-03-10 OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms Hao, Yanqi Merkoulovitch, Anna Vlasblom, James Pu, Shuye Turinsky, Andrei L. Roudeva, Denitza Turner, Brian Greenblatt, Jack Wodak, Shoshana J. Bioinformatics Applications Note Motivation: Protein interaction networks contain a wealth of biological information, but their large size often hinders cross-organism comparisons. We present OrthoNets, a Cytoscape plugin that displays protein–protein interaction (PPI) networks from two organisms simultaneously, highlighting orthology relationships and aggregating several types of biomedical annotations. OrthoNets also allows PPI networks derived from experiments to be overlaid on networks extracted from public databases, supporting the identification and verification of new interactors. Any newly identified PPIs can be validated by checking whether their orthologs interact in another organism. Availability: OrthoNets is freely available at http://wodaklab.org/orthonets/. Contact: jim.vlasblom@utoronto.ca Oxford University Press 2011-03-15 2011-01-20 /pmc/articles/PMC3051336/ /pubmed/21257609 http://dx.doi.org/10.1093/bioinformatics/btr035 Text en © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Note
Hao, Yanqi
Merkoulovitch, Anna
Vlasblom, James
Pu, Shuye
Turinsky, Andrei L.
Roudeva, Denitza
Turner, Brian
Greenblatt, Jack
Wodak, Shoshana J.
OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms
title OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms
title_full OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms
title_fullStr OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms
title_full_unstemmed OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms
title_short OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms
title_sort orthonets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3051336/
https://www.ncbi.nlm.nih.gov/pubmed/21257609
http://dx.doi.org/10.1093/bioinformatics/btr035
work_keys_str_mv AT haoyanqi orthonetssimultaneousvisualanalysisoforthologsandtheirinteractionneighborhoodsacrossdifferentorganisms
AT merkoulovitchanna orthonetssimultaneousvisualanalysisoforthologsandtheirinteractionneighborhoodsacrossdifferentorganisms
AT vlasblomjames orthonetssimultaneousvisualanalysisoforthologsandtheirinteractionneighborhoodsacrossdifferentorganisms
AT pushuye orthonetssimultaneousvisualanalysisoforthologsandtheirinteractionneighborhoodsacrossdifferentorganisms
AT turinskyandreil orthonetssimultaneousvisualanalysisoforthologsandtheirinteractionneighborhoodsacrossdifferentorganisms
AT roudevadenitza orthonetssimultaneousvisualanalysisoforthologsandtheirinteractionneighborhoodsacrossdifferentorganisms
AT turnerbrian orthonetssimultaneousvisualanalysisoforthologsandtheirinteractionneighborhoodsacrossdifferentorganisms
AT greenblattjack orthonetssimultaneousvisualanalysisoforthologsandtheirinteractionneighborhoodsacrossdifferentorganisms
AT wodakshoshanaj orthonetssimultaneousvisualanalysisoforthologsandtheirinteractionneighborhoodsacrossdifferentorganisms

Ejemplares similares