QServer: a biclustering server for prediction and assessment of co-expressed gene clusters.

<h4>Background</h4>Biclustering is a powerful technique for identification of co-expressed gene groups under any (unspecified) substantial subset of given experimental conditions, which can be used for elucidation of transcriptionally co-regulated genes.<h4>Results</h4>We hav...

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Autores principales:	Fengfeng Zhou, Qin Ma, Guojun Li, Ying Xu
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/dd7d070aeee94400b8722c9831bf9644
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spelling	oai:doaj.org-article:dd7d070aeee94400b8722c9831bf96442021-11-18T07:26:04ZQServer: a biclustering server for prediction and assessment of co-expressed gene clusters.1932-620310.1371/journal.pone.0032660https://doaj.org/article/dd7d070aeee94400b8722c9831bf96442012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22403692/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>Biclustering is a powerful technique for identification of co-expressed gene groups under any (unspecified) substantial subset of given experimental conditions, which can be used for elucidation of transcriptionally co-regulated genes.<h4>Results</h4>We have previously developed a biclustering algorithm, QUBIC, which can solve more general biclustering problems than previous biclustering algorithms. To fully utilize the analysis power the algorithm provides, we have developed a web server, QServer, for prediction, computational validation and analyses of co-expressed gene clusters. Specifically, the QServer has the following capabilities in addition to biclustering by QUBIC: (i) prediction and assessment of conserved cis regulatory motifs in promoter sequences of the predicted co-expressed genes; (ii) functional enrichment analyses of the predicted co-expressed gene clusters using Gene Ontology (GO) terms, and (iii) visualization capabilities in support of interactive biclustering analyses. QServer supports the biclustering and functional analysis for a wide range of organisms, including human, mouse, Arabidopsis, bacteria and archaea, whose underlying genome database will be continuously updated.<h4>Conclusion</h4>We believe that QServer provides an easy-to-use and highly effective platform useful for hypothesis formulation and testing related to transcription co-regulation.Fengfeng ZhouQin MaGuojun LiYing XuPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 3, p e32660 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Fengfeng Zhou Qin Ma Guojun Li Ying Xu QServer: a biclustering server for prediction and assessment of co-expressed gene clusters.
description	<h4>Background</h4>Biclustering is a powerful technique for identification of co-expressed gene groups under any (unspecified) substantial subset of given experimental conditions, which can be used for elucidation of transcriptionally co-regulated genes.<h4>Results</h4>We have previously developed a biclustering algorithm, QUBIC, which can solve more general biclustering problems than previous biclustering algorithms. To fully utilize the analysis power the algorithm provides, we have developed a web server, QServer, for prediction, computational validation and analyses of co-expressed gene clusters. Specifically, the QServer has the following capabilities in addition to biclustering by QUBIC: (i) prediction and assessment of conserved cis regulatory motifs in promoter sequences of the predicted co-expressed genes; (ii) functional enrichment analyses of the predicted co-expressed gene clusters using Gene Ontology (GO) terms, and (iii) visualization capabilities in support of interactive biclustering analyses. QServer supports the biclustering and functional analysis for a wide range of organisms, including human, mouse, Arabidopsis, bacteria and archaea, whose underlying genome database will be continuously updated.<h4>Conclusion</h4>We believe that QServer provides an easy-to-use and highly effective platform useful for hypothesis formulation and testing related to transcription co-regulation.
format	article
author	Fengfeng Zhou Qin Ma Guojun Li Ying Xu
author_facet	Fengfeng Zhou Qin Ma Guojun Li Ying Xu
author_sort	Fengfeng Zhou
title	QServer: a biclustering server for prediction and assessment of co-expressed gene clusters.
title_short	QServer: a biclustering server for prediction and assessment of co-expressed gene clusters.
title_full	QServer: a biclustering server for prediction and assessment of co-expressed gene clusters.
title_fullStr	QServer: a biclustering server for prediction and assessment of co-expressed gene clusters.
title_full_unstemmed	QServer: a biclustering server for prediction and assessment of co-expressed gene clusters.
title_sort	qserver: a biclustering server for prediction and assessment of co-expressed gene clusters.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/dd7d070aeee94400b8722c9831bf9644
work_keys_str_mv	AT fengfengzhou qserverabiclusteringserverforpredictionandassessmentofcoexpressedgeneclusters AT qinma qserverabiclusteringserverforpredictionandassessmentofcoexpressedgeneclusters AT guojunli qserverabiclusteringserverforpredictionandassessmentofcoexpressedgeneclusters AT yingxu qserverabiclusteringserverforpredictionandassessmentofcoexpressedgeneclusters
_version_	1718423502915108864

QServer: a biclustering server for prediction and assessment of co-expressed gene clusters.

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