Gene set-based module discovery decodes cis-regulatory codes governing diverse gene expression across human multiple tissues.

Decoding transcriptional programs governing transcriptomic diversity across human multiple tissues is a major challenge in bioinformatics. To address this problem, a number of computational methods have focused on cis-regulatory codes driving overexpression or underexpression in a single tissue as c...

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Autores principales:	Atsushi Niida, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, Satoru Miyano
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2010
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/e6df0a15df8b4d05a5e5feeb618c6be2
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spelling	oai:doaj.org-article:e6df0a15df8b4d05a5e5feeb618c6be22021-12-02T20:21:04ZGene set-based module discovery decodes cis-regulatory codes governing diverse gene expression across human multiple tissues.1932-620310.1371/journal.pone.0010910https://doaj.org/article/e6df0a15df8b4d05a5e5feeb618c6be22010-06-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20544005/?tool=EBIhttps://doaj.org/toc/1932-6203Decoding transcriptional programs governing transcriptomic diversity across human multiple tissues is a major challenge in bioinformatics. To address this problem, a number of computational methods have focused on cis-regulatory codes driving overexpression or underexpression in a single tissue as compared to others. On the other hand, we recently proposed a different approach to mine cis-regulatory codes: starting from gene sets sharing common cis-regulatory motifs, the method screens for expression modules based on expression coherence. However, both approaches seem to be insufficient to capture transcriptional programs that control gene expression in a subset of all samples. Especially, this limitation would be serious when analyzing multiple tissue data. To overcome this limitation, we developed a new module discovery method termed BEEM (Biclusering-based Extraction of Expression Modules) in order to discover expression modules that are functional in a subset of tissues. We showed that, when applied to expression profiles of human multiple tissues, BEEM finds expression modules missed by two existing approaches that are based on the coherent expression and the single tissue-specific differential expression. From the BEEM results, we obtained new insights into transcriptional programs controlling transcriptomic diversity across various types of tissues. This study introduces BEEM as a powerful tool for decoding regulatory programs from a compendium of gene expression profiles.Atsushi NiidaSeiya ImotoRui YamaguchiMasao NagasakiSatoru MiyanoPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 5, Iss 6, p e10910 (2010)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Atsushi Niida Seiya Imoto Rui Yamaguchi Masao Nagasaki Satoru Miyano Gene set-based module discovery decodes cis-regulatory codes governing diverse gene expression across human multiple tissues.
description	Decoding transcriptional programs governing transcriptomic diversity across human multiple tissues is a major challenge in bioinformatics. To address this problem, a number of computational methods have focused on cis-regulatory codes driving overexpression or underexpression in a single tissue as compared to others. On the other hand, we recently proposed a different approach to mine cis-regulatory codes: starting from gene sets sharing common cis-regulatory motifs, the method screens for expression modules based on expression coherence. However, both approaches seem to be insufficient to capture transcriptional programs that control gene expression in a subset of all samples. Especially, this limitation would be serious when analyzing multiple tissue data. To overcome this limitation, we developed a new module discovery method termed BEEM (Biclusering-based Extraction of Expression Modules) in order to discover expression modules that are functional in a subset of tissues. We showed that, when applied to expression profiles of human multiple tissues, BEEM finds expression modules missed by two existing approaches that are based on the coherent expression and the single tissue-specific differential expression. From the BEEM results, we obtained new insights into transcriptional programs controlling transcriptomic diversity across various types of tissues. This study introduces BEEM as a powerful tool for decoding regulatory programs from a compendium of gene expression profiles.
format	article
author	Atsushi Niida Seiya Imoto Rui Yamaguchi Masao Nagasaki Satoru Miyano
author_facet	Atsushi Niida Seiya Imoto Rui Yamaguchi Masao Nagasaki Satoru Miyano
author_sort	Atsushi Niida
title	Gene set-based module discovery decodes cis-regulatory codes governing diverse gene expression across human multiple tissues.
title_short	Gene set-based module discovery decodes cis-regulatory codes governing diverse gene expression across human multiple tissues.
title_full	Gene set-based module discovery decodes cis-regulatory codes governing diverse gene expression across human multiple tissues.
title_fullStr	Gene set-based module discovery decodes cis-regulatory codes governing diverse gene expression across human multiple tissues.
title_full_unstemmed	Gene set-based module discovery decodes cis-regulatory codes governing diverse gene expression across human multiple tissues.
title_sort	gene set-based module discovery decodes cis-regulatory codes governing diverse gene expression across human multiple tissues.
publisher	Public Library of Science (PLoS)
publishDate	2010
url	https://doaj.org/article/e6df0a15df8b4d05a5e5feeb618c6be2
work_keys_str_mv	AT atsushiniida genesetbasedmodulediscoverydecodescisregulatorycodesgoverningdiversegeneexpressionacrosshumanmultipletissues AT seiyaimoto genesetbasedmodulediscoverydecodescisregulatorycodesgoverningdiversegeneexpressionacrosshumanmultipletissues AT ruiyamaguchi genesetbasedmodulediscoverydecodescisregulatorycodesgoverningdiversegeneexpressionacrosshumanmultipletissues AT masaonagasaki genesetbasedmodulediscoverydecodescisregulatorycodesgoverningdiversegeneexpressionacrosshumanmultipletissues AT satorumiyano genesetbasedmodulediscoverydecodescisregulatorycodesgoverningdiversegeneexpressionacrosshumanmultipletissues
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Gene set-based module discovery decodes cis-regulatory codes governing diverse gene expression across human multiple tissues.

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