Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Soul, Jamie, Dunn, Sara L., Hardingham, Tim E., Boot-Handford, Ray P., Schwartz, Jean-Marc
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
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
_version_ 1782483130001653760
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
work_keys_str_mv AT souljamie phenomescapeacytoscapeapptoidentifydifferentiallyregulatedsubnetworksusingknowndiseaseassociations
AT dunnsaral phenomescapeacytoscapeapptoidentifydifferentiallyregulatedsubnetworksusingknowndiseaseassociations
AT hardinghamtime phenomescapeacytoscapeapptoidentifydifferentiallyregulatedsubnetworksusingknowndiseaseassociations
AT boothandfordrayp phenomescapeacytoscapeapptoidentifydifferentiallyregulatedsubnetworksusingknowndiseaseassociations
AT schwartzjeanmarc phenomescapeacytoscapeapptoidentifydifferentiallyregulatedsubnetworksusingknowndiseaseassociations