Computational search for over-represented 8-mers within the 5'-regulatory regions of 634 mouse testis-specific genes.
Identifieur interne : 002A25 ( Main/Merge ); précédent : 002A24; suivant : 002A26Computational search for over-represented 8-mers within the 5'-regulatory regions of 634 mouse testis-specific genes.
Auteurs : Akifumi Yamashita [Japon] ; Naohisa Goto ; Seiji Nishiguchi ; Kazunori Shimada ; Hiromichi Yamanishi ; Teruo YasunagaSource :
- Gene [ 0378-1119 ] ; 2008.
Descripteurs français
- KwdFr :
- AMP cyclique (métabolisme), Analyse de profil d'expression de gènes, Animaux, Biologie informatique (), Modèles biologiques, Modèles génétiques, Modèles statistiques, Mâle, Régions promotrices (génétique), Souris, Séquences d'acides nucléiques régulatrices, Séquençage par oligonucléotides en batterie, Testicule (métabolisme), Transcription génétique, Éléments de réponse.
- MESH :
- métabolisme : AMP cyclique, Testicule.
- Analyse de profil d'expression de gènes, Animaux, Biologie informatique, Modèles biologiques, Modèles génétiques, Modèles statistiques, Mâle, Régions promotrices (génétique), Souris, Séquences d'acides nucléiques régulatrices, Séquençage par oligonucléotides en batterie, Transcription génétique, Éléments de réponse.
English descriptors
- KwdEn :
- Animals, Computational Biology (methods), Cyclic AMP (metabolism), Gene Expression Profiling, Male, Mice, Models, Biological, Models, Genetic, Models, Statistical, Oligonucleotide Array Sequence Analysis, Promoter Regions, Genetic, Regulatory Sequences, Nucleic Acid, Response Elements, Testis (metabolism), Transcription, Genetic.
- MESH :
- chemical , metabolism : Cyclic AMP.
- metabolism : Testis.
- methods : Computational Biology.
- Animals, Gene Expression Profiling, Male, Mice, Models, Biological, Models, Genetic, Models, Statistical, Oligonucleotide Array Sequence Analysis, Promoter Regions, Genetic, Regulatory Sequences, Nucleic Acid, Response Elements, Transcription, Genetic.
Abstract
Accumulation of microarray data has enabled the computational analysis of gene expressions in various tissues. Although the genes showing testis-specific expression are most abundant among the genes exhibiting tissue-specific expression, no systematic study has been conducted for over-represented motifs within their regulatory regions. We have identified 117 over-represented 8-mers that appeared 2648 times within the regulatory regions of 634 testis-specific genes. Of these, 64 over-represented 8-mers were significantly more frequent in the regulatory regions of testis-specific genes than in those of non-testis-specific genes. In this group of 8-mers, 4 8-mers differed from the canonical cAMP response element (CRE) 8-mer by 1 letter, but the canonical CRE was not included in this group. We consider that CRE-like 8-mers participate in the regulatory expression of testis-specific genes to a greater extent than the canonical CRE 8-mer.
DOI: 10.1016/j.gene.2008.08.018
PubMed: 18817858
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pubmed:18817858Le document en format XML
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last="Goto">Naohisa Goto</name></author><author><name sortKey="Nishiguchi, Seiji" sort="Nishiguchi, Seiji" uniqKey="Nishiguchi S" first="Seiji" last="Nishiguchi">Seiji Nishiguchi</name></author><author><name sortKey="Shimada, Kazunori" sort="Shimada, Kazunori" uniqKey="Shimada K" first="Kazunori" last="Shimada">Kazunori Shimada</name></author><author><name sortKey="Yamanishi, Hiromichi" sort="Yamanishi, Hiromichi" uniqKey="Yamanishi H" first="Hiromichi" last="Yamanishi">Hiromichi Yamanishi</name></author><author><name sortKey="Yasunaga, Teruo" sort="Yasunaga, Teruo" uniqKey="Yasunaga T" first="Teruo" last="Yasunaga">Teruo Yasunaga</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2008">2008</date><idno type="RBID">pubmed:18817858</idno><idno type="pmid">18817858</idno><idno type="doi">10.1016/j.gene.2008.08.018</idno><idno type="wicri:Area/PubMed/Corpus">002074</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" 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wicri:level="1"><nlm:affiliation>Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871</wicri:regionArea><wicri:noRegion>Osaka 565-0871</wicri:noRegion></affiliation></author><author><name sortKey="Goto, Naohisa" sort="Goto, Naohisa" uniqKey="Goto N" first="Naohisa" last="Goto">Naohisa Goto</name></author><author><name sortKey="Nishiguchi, Seiji" sort="Nishiguchi, Seiji" uniqKey="Nishiguchi S" first="Seiji" last="Nishiguchi">Seiji Nishiguchi</name></author><author><name sortKey="Shimada, Kazunori" sort="Shimada, Kazunori" uniqKey="Shimada K" first="Kazunori" last="Shimada">Kazunori Shimada</name></author><author><name sortKey="Yamanishi, Hiromichi" sort="Yamanishi, Hiromichi" uniqKey="Yamanishi H" first="Hiromichi" last="Yamanishi">Hiromichi Yamanishi</name></author><author><name sortKey="Yasunaga, Teruo" sort="Yasunaga, Teruo" uniqKey="Yasunaga T" first="Teruo" last="Yasunaga">Teruo Yasunaga</name></author></analytic><series><title level="j">Gene</title><idno type="ISSN">0378-1119</idno><imprint><date when="2008" type="published">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Computational Biology (methods)</term><term>Cyclic AMP (metabolism)</term><term>Gene Expression Profiling</term><term>Male</term><term>Mice</term><term>Models, Biological</term><term>Models, Genetic</term><term>Models, Statistical</term><term>Oligonucleotide Array Sequence Analysis</term><term>Promoter Regions, Genetic</term><term>Regulatory Sequences, Nucleic Acid</term><term>Response Elements</term><term>Testis 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qualifier="métabolisme" xml:lang="fr"><term>AMP cyclique</term><term>Testicule</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Gene Expression Profiling</term><term>Male</term><term>Mice</term><term>Models, Biological</term><term>Models, Genetic</term><term>Models, Statistical</term><term>Oligonucleotide Array Sequence Analysis</term><term>Promoter Regions, Genetic</term><term>Regulatory Sequences, Nucleic Acid</term><term>Response Elements</term><term>Transcription, Genetic</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Animaux</term><term>Biologie informatique</term><term>Modèles biologiques</term><term>Modèles génétiques</term><term>Modèles statistiques</term><term>Mâle</term><term>Régions promotrices (génétique)</term><term>Souris</term><term>Séquences d'acides nucléiques régulatrices</term><term>Séquençage par oligonucléotides en batterie</term><term>Transcription 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Although the genes showing testis-specific expression are most abundant among the genes exhibiting tissue-specific expression, no systematic study has been conducted for over-represented motifs within their regulatory regions. We have identified 117 over-represented 8-mers that appeared 2648 times within the regulatory regions of 634 testis-specific genes. Of these, 64 over-represented 8-mers were significantly more frequent in the regulatory regions of testis-specific genes than in those of non-testis-specific genes. In this group of 8-mers, 4 8-mers differed from the canonical cAMP response element (CRE) 8-mer by 1 letter, but the canonical CRE was not included in this group. We consider that CRE-like 8-mers participate in the regulatory expression of testis-specific genes to a greater extent than the canonical CRE 8-mer.</div></front></TEI></record>Pour manipuler ce document sous Unix (Dilib)
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