PathwAX: a web server for network crosstalk based pathway annotation

Pathway annotation of gene lists is often used to functionally analyse biomolecular data such as gene expression in order to establish which processes are activated in a given experiment. Databases such as KEGG or GO represent collections of how genes are known to be organized in pathways, and the c...

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Main Authors:	Ogris, Christoph, Helleday, Thomas, Sonnhammer, Erik L.L.
Format:	Online
Language:	English
Published:	Oxford University Press 2016
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987909/

id	pubmed-4987909
recordtype	oai_dc
spelling	pubmed-49879092016-08-22 PathwAX: a web server for network crosstalk based pathway annotation Ogris, Christoph Helleday, Thomas Sonnhammer, Erik L.L. Web Server issue Pathway annotation of gene lists is often used to functionally analyse biomolecular data such as gene expression in order to establish which processes are activated in a given experiment. Databases such as KEGG or GO represent collections of how genes are known to be organized in pathways, and the challenge is to compare a given gene list with the known pathways such that all true relations are identified. Most tools apply statistical measures to the gene overlap between the gene list and pathway. It is however problematic to avoid false negatives and false positives when only using the gene overlap. The pathwAX web server (http://pathwAX.sbc.su.se/) applies a different approach which is based on network crosstalk. It uses the comprehensive network FunCoup to analyse network crosstalk between a query gene list and KEGG pathways. PathwAX runs the BinoX algorithm, which employs Monte-Carlo sampling of randomized networks and estimates a binomial distribution, for estimating the statistical significance of the crosstalk. This results in substantially higher accuracy than gene overlap methods. The system was optimized for speed and allows interactive web usage. We illustrate the usage and output of pathwAX. Oxford University Press 2016-07-08 2016-05-05 /pmc/articles/PMC4987909/ /pubmed/27151197 http://dx.doi.org/10.1093/nar/gkw356 Text en © The Author(s) 2016. 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
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Ogris, Christoph Helleday, Thomas Sonnhammer, Erik L.L.
spellingShingle	Ogris, Christoph Helleday, Thomas Sonnhammer, Erik L.L. PathwAX: a web server for network crosstalk based pathway annotation
author_facet	Ogris, Christoph Helleday, Thomas Sonnhammer, Erik L.L.
author_sort	Ogris, Christoph
title	PathwAX: a web server for network crosstalk based pathway annotation
title_short	PathwAX: a web server for network crosstalk based pathway annotation
title_full	PathwAX: a web server for network crosstalk based pathway annotation
title_fullStr	PathwAX: a web server for network crosstalk based pathway annotation
title_full_unstemmed	PathwAX: a web server for network crosstalk based pathway annotation
title_sort	pathwax: a web server for network crosstalk based pathway annotation
description	Pathway annotation of gene lists is often used to functionally analyse biomolecular data such as gene expression in order to establish which processes are activated in a given experiment. Databases such as KEGG or GO represent collections of how genes are known to be organized in pathways, and the challenge is to compare a given gene list with the known pathways such that all true relations are identified. Most tools apply statistical measures to the gene overlap between the gene list and pathway. It is however problematic to avoid false negatives and false positives when only using the gene overlap. The pathwAX web server (http://pathwAX.sbc.su.se/) applies a different approach which is based on network crosstalk. It uses the comprehensive network FunCoup to analyse network crosstalk between a query gene list and KEGG pathways. PathwAX runs the BinoX algorithm, which employs Monte-Carlo sampling of randomized networks and estimates a binomial distribution, for estimating the statistical significance of the crosstalk. This results in substantially higher accuracy than gene overlap methods. The system was optimized for speed and allows interactive web usage. We illustrate the usage and output of pathwAX.
publisher	Oxford University Press
publishDate	2016
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987909/
_version_	1613628896938295296

PathwAX: a web server for network crosstalk based pathway annotation

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