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PhenomeScape: a cytoscape app to identify differentially regulated sub-networks using known disease associations
Summary: PhenomeScape is a Cytoscape app which provides easy access to the PhenomeExpress algorithm to interpret gene expression data. PhenomeExpress integrates protein interaction networks with known phenotype to gene associations to find active sub-networks enriched in differentially expressed gen...
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/PMC5167065/ https://www.ncbi.nlm.nih.gov/pubmed/27559157 http://dx.doi.org/10.1093/bioinformatics/btw545 |
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author | Soul, Jamie Dunn, Sara L. Hardingham, Tim E. Boot-Handford, Ray P. Schwartz, Jean-Marc |
author_facet | Soul, Jamie Dunn, Sara L. Hardingham, Tim E. Boot-Handford, Ray P. Schwartz, Jean-Marc |
author_sort | Soul, Jamie |
collection | PubMed |
description | Summary: PhenomeScape is a Cytoscape app which provides easy access to the PhenomeExpress algorithm to interpret gene expression data. PhenomeExpress integrates protein interaction networks with known phenotype to gene associations to find active sub-networks enriched in differentially expressed genes. It also incorporates cross-species phenotypes and associations to include results from animal models of disease. With expression data imported into PhenomeScape, the user can quickly generate and visualise interactive sub-networks. PhenomeScape thus enables researchers to use prior knowledge of a disease to identify differentially regulated sub-networks and to generate an overview of altered biologically processes specific to that disease. Availability and Implementation: Freely available for download at https://github.com/soulj/PhenomeScape Contact: jamie.soul@postgrad.manchester.ac.uk or jean-marc.schwartz@manchester.ac.uk |
format | Online Article Text |
id | pubmed-5167065 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-51670652016-12-20 PhenomeScape: a cytoscape app to identify differentially regulated sub-networks using known disease associations Soul, Jamie Dunn, Sara L. Hardingham, Tim E. Boot-Handford, Ray P. Schwartz, Jean-Marc Bioinformatics Applications Notes Summary: PhenomeScape is a Cytoscape app which provides easy access to the PhenomeExpress algorithm to interpret gene expression data. PhenomeExpress integrates protein interaction networks with known phenotype to gene associations to find active sub-networks enriched in differentially expressed genes. It also incorporates cross-species phenotypes and associations to include results from animal models of disease. With expression data imported into PhenomeScape, the user can quickly generate and visualise interactive sub-networks. PhenomeScape thus enables researchers to use prior knowledge of a disease to identify differentially regulated sub-networks and to generate an overview of altered biologically processes specific to that disease. Availability and Implementation: Freely available for download at https://github.com/soulj/PhenomeScape Contact: jamie.soul@postgrad.manchester.ac.uk or jean-marc.schwartz@manchester.ac.uk Oxford University Press 2016-12-15 2016-08-24 /pmc/articles/PMC5167065/ /pubmed/27559157 http://dx.doi.org/10.1093/bioinformatics/btw545 Text en © The Author 2016. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Applications Notes Soul, Jamie Dunn, Sara L. Hardingham, Tim E. Boot-Handford, Ray P. Schwartz, Jean-Marc PhenomeScape: a cytoscape app to identify differentially regulated sub-networks using known disease associations |
title | PhenomeScape: a cytoscape app to identify differentially regulated sub-networks using known disease associations |
title_full | PhenomeScape: a cytoscape app to identify differentially regulated sub-networks using known disease associations |
title_fullStr | PhenomeScape: a cytoscape app to identify differentially regulated sub-networks using known disease associations |
title_full_unstemmed | PhenomeScape: a cytoscape app to identify differentially regulated sub-networks using known disease associations |
title_short | PhenomeScape: a cytoscape app to identify differentially regulated sub-networks using known disease associations |
title_sort | phenomescape: a cytoscape app to identify differentially regulated sub-networks using known disease associations |
topic | Applications Notes |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5167065/ https://www.ncbi.nlm.nih.gov/pubmed/27559157 http://dx.doi.org/10.1093/bioinformatics/btw545 |
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