Integrated pathway clusters with coherent biological themes for target prioritisation.

Prioritising candidate genes for further experimental characterisation is an essential, yet challenging task in biomedical research. One way of achieving this goal is to identify specific biological themes that are enriched within the gene set of interest to obtain insights into the biological pheno...

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Autores principales:	Yi-An Chen, Lokesh P Tripathi, Benoit H Dessailly, Johan Nyström-Persson, Shandar Ahmad, Kenji Mizuguchi
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/012ece2142ca4a7aa4dd881c14992167
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spelling	oai:doaj.org-article:012ece2142ca4a7aa4dd881c149921672021-11-18T08:16:06ZIntegrated pathway clusters with coherent biological themes for target prioritisation.1932-620310.1371/journal.pone.0099030https://doaj.org/article/012ece2142ca4a7aa4dd881c149921672014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24918583/?tool=EBIhttps://doaj.org/toc/1932-6203Prioritising candidate genes for further experimental characterisation is an essential, yet challenging task in biomedical research. One way of achieving this goal is to identify specific biological themes that are enriched within the gene set of interest to obtain insights into the biological phenomena under study. Biological pathway data have been particularly useful in identifying functional associations of genes and/or gene sets. However, biological pathway information as compiled in varied repositories often differs in scope and content, preventing a more effective and comprehensive characterisation of gene sets. Here we describe a new approach to constructing biologically coherent gene sets from pathway data in major public repositories and employing them for functional analysis of large gene sets. We first revealed significant overlaps in gene content between different pathways and then defined a clustering method based on the shared gene content and the similarity of gene overlap patterns. We established the biological relevance of the constructed pathway clusters using independent quantitative measures and we finally demonstrated the effectiveness of the constructed pathway clusters in comparative functional enrichment analysis of gene sets associated with diverse human diseases gathered from the literature. The pathway clusters and gene mappings have been integrated into the TargetMine data warehouse and are likely to provide a concise, manageable and biologically relevant means of functional analysis of gene sets and to facilitate candidate gene prioritisation.Yi-An ChenLokesh P TripathiBenoit H DessaillyJohan Nyström-PerssonShandar AhmadKenji MizuguchiPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 6, p e99030 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Yi-An Chen Lokesh P Tripathi Benoit H Dessailly Johan Nyström-Persson Shandar Ahmad Kenji Mizuguchi Integrated pathway clusters with coherent biological themes for target prioritisation.
description	Prioritising candidate genes for further experimental characterisation is an essential, yet challenging task in biomedical research. One way of achieving this goal is to identify specific biological themes that are enriched within the gene set of interest to obtain insights into the biological phenomena under study. Biological pathway data have been particularly useful in identifying functional associations of genes and/or gene sets. However, biological pathway information as compiled in varied repositories often differs in scope and content, preventing a more effective and comprehensive characterisation of gene sets. Here we describe a new approach to constructing biologically coherent gene sets from pathway data in major public repositories and employing them for functional analysis of large gene sets. We first revealed significant overlaps in gene content between different pathways and then defined a clustering method based on the shared gene content and the similarity of gene overlap patterns. We established the biological relevance of the constructed pathway clusters using independent quantitative measures and we finally demonstrated the effectiveness of the constructed pathway clusters in comparative functional enrichment analysis of gene sets associated with diverse human diseases gathered from the literature. The pathway clusters and gene mappings have been integrated into the TargetMine data warehouse and are likely to provide a concise, manageable and biologically relevant means of functional analysis of gene sets and to facilitate candidate gene prioritisation.
format	article
author	Yi-An Chen Lokesh P Tripathi Benoit H Dessailly Johan Nyström-Persson Shandar Ahmad Kenji Mizuguchi
author_facet	Yi-An Chen Lokesh P Tripathi Benoit H Dessailly Johan Nyström-Persson Shandar Ahmad Kenji Mizuguchi
author_sort	Yi-An Chen
title	Integrated pathway clusters with coherent biological themes for target prioritisation.
title_short	Integrated pathway clusters with coherent biological themes for target prioritisation.
title_full	Integrated pathway clusters with coherent biological themes for target prioritisation.
title_fullStr	Integrated pathway clusters with coherent biological themes for target prioritisation.
title_full_unstemmed	Integrated pathway clusters with coherent biological themes for target prioritisation.
title_sort	integrated pathway clusters with coherent biological themes for target prioritisation.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/012ece2142ca4a7aa4dd881c14992167
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_version_	1718421962475175936

Integrated pathway clusters with coherent biological themes for target prioritisation.

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