Identification of key mechanisms controlling gene expression in Leishmania infected macrophages using genome-wide promoter analysis.
Identifieur interne : 000115 ( Main/Exploration ); précédent : 000114; suivant : 000116Identification of key mechanisms controlling gene expression in Leishmania infected macrophages using genome-wide promoter analysis.
Auteurs : Kais Ghedira [Tunisie] ; Klaus Hornischer ; Tatiana Konovalova ; Ahmed-Zaki Jenhani ; Alia Benkahla ; Alexander KelSource :
- Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases [ 1567-7257 ] ; 2011.
Descripteurs français
- KwdFr :
- Analyse de profil d'expression de gènes (MeSH), Animaux (MeSH), Bases de données génétiques (MeSH), Biologie informatique (MeSH), Chiens (MeSH), Facteurs de transcription (métabolisme), Humains (MeSH), Leishmania (physiologie), Leishmaniose (physiopathologie), Macrophages (métabolisme), Macrophages (parasitologie), Pan troglodytes (MeSH), Rats (MeSH), Régions promotrices (génétique) (génétique), Régulation de l'expression des gènes (MeSH), Réseaux de régulation génique (génétique), Sites de fixation (génétique), Souris (MeSH), Voies et réseaux métaboliques (génétique), Étude d'association pangénomique (MeSH).
- MESH :
- génétique : Régions promotrices (génétique), Réseaux de régulation génique, Sites de fixation, Voies et réseaux métaboliques.
- métabolisme : Facteurs de transcription, Macrophages.
- parasitologie : Macrophages.
- physiologie : Leishmania.
- physiopathologie : Leishmaniose.
- Analyse de profil d'expression de gènes, Animaux, Bases de données génétiques, Biologie informatique, Chiens, Humains, Pan troglodytes, Rats, Régulation de l'expression des gènes, Souris, Étude d'association pangénomique.
English descriptors
- KwdEn :
- Animals (MeSH), Binding Sites (genetics), Computational Biology (MeSH), Databases, Genetic (MeSH), Dogs (MeSH), Gene Expression Profiling (MeSH), Gene Expression Regulation (MeSH), Gene Regulatory Networks (genetics), Genome-Wide Association Study (MeSH), Humans (MeSH), Leishmania (physiology), Leishmaniasis (physiopathology), Macrophages (metabolism), Macrophages (parasitology), Metabolic Networks and Pathways (genetics), Mice (MeSH), Pan troglodytes (MeSH), Promoter Regions, Genetic (genetics), Rats (MeSH), Transcription Factors (metabolism).
- MESH :
- chemical , metabolism : Transcription Factors.
- genetics : Binding Sites, Gene Regulatory Networks, Metabolic Networks and Pathways, Promoter Regions, Genetic.
- metabolism : Macrophages.
- parasitology : Macrophages.
- physiology : Leishmania.
- physiopathology : Leishmaniasis.
- Animals, Computational Biology, Databases, Genetic, Dogs, Gene Expression Profiling, Gene Expression Regulation, Genome-Wide Association Study, Humans, Mice, Pan troglodytes, Rats.
Abstract
The present study describes the in silico prediction of the regulatory network of Leishmania infected human macrophages. The construction of the gene regulatory network requires the identification of Transcription Factor Binding Sites (TFBSs) in the regulatory regions (promoters, enhancers) of genes that are regulated upon Leishmania infection. The promoters of human, mouse, rat, dog and chimpanzee genes were first identified in the whole genomes using available experimental data on full length cDNA sequences or deep CAGE tag data (DBTSS, FANTOM3, FANTOM4), mRNA models (ENSEMBL), or using hand annotated data (EPD, TRANSFAC). A phylogenetic footprinting analysis and a MATCH analysis of the promoter sequences were then performed to predict TFBS. Then, an SQL database that integrates all results of promoter analysis as well as other genome annotation information obtained from ENSEMBL, TRANSFAC, TRED (Transcription Regulatory Element Database), ORegAnno and the ENCODE project, was established. Finally publicly available expression data from human Leishmania infected macrophages were analyzed using the genome-wide information on predicted TFBS with the computer system ExPlain™. The gene regulatory network was constructed and activated signal transduction pathways were revealed. The Irak1 pathway was identified as a key pathway regulating gene expression changes in Leishmania infected macrophages.
DOI: 10.1016/j.meegid.2010.10.015
PubMed: 21093613
Affiliations:
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Le document en format XML
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Hornischer</name></author><author><name sortKey="Konovalova, Tatiana" sort="Konovalova, Tatiana" uniqKey="Konovalova T" first="Tatiana" last="Konovalova">Tatiana Konovalova</name></author><author><name sortKey="Jenhani, Ahmed Zaki" sort="Jenhani, Ahmed Zaki" uniqKey="Jenhani A" first="Ahmed-Zaki" last="Jenhani">Ahmed-Zaki Jenhani</name></author><author><name sortKey="Benkahla, Alia" sort="Benkahla, Alia" uniqKey="Benkahla A" first="Alia" last="Benkahla">Alia Benkahla</name></author><author><name sortKey="Kel, Alexander" sort="Kel, Alexander" uniqKey="Kel A" first="Alexander" last="Kel">Alexander Kel</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2011">2011</date><idno type="RBID">pubmed:21093613</idno><idno type="pmid">21093613</idno><idno type="doi">10.1016/j.meegid.2010.10.015</idno><idno type="wicri:Area/PubMed/Corpus">000702</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" 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Tunisia.</nlm:affiliation><country xml:lang="fr">Tunisie</country><wicri:regionArea>Laboratory of Immunology, Vaccinology, and Molecular Genetics, Institut Pasteur de Tunis, 13 place Pasteur BP 74, Tunis</wicri:regionArea><placeName><settlement type="city">Tunis</settlement><region nuts="2">Gouvernorat de Tunis</region></placeName></affiliation></author><author><name sortKey="Hornischer, Klaus" sort="Hornischer, Klaus" uniqKey="Hornischer K" first="Klaus" last="Hornischer">Klaus Hornischer</name></author><author><name sortKey="Konovalova, Tatiana" sort="Konovalova, Tatiana" uniqKey="Konovalova T" first="Tatiana" last="Konovalova">Tatiana Konovalova</name></author><author><name sortKey="Jenhani, Ahmed Zaki" sort="Jenhani, Ahmed Zaki" uniqKey="Jenhani A" first="Ahmed-Zaki" last="Jenhani">Ahmed-Zaki Jenhani</name></author><author><name sortKey="Benkahla, Alia" sort="Benkahla, Alia" uniqKey="Benkahla A" first="Alia" last="Benkahla">Alia Benkahla</name></author><author><name sortKey="Kel, Alexander" sort="Kel, Alexander" uniqKey="Kel A" first="Alexander" last="Kel">Alexander Kel</name></author></analytic><series><title level="j">Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases</title><idno type="eISSN">1567-7257</idno><imprint><date when="2011" type="published">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals (MeSH)</term><term>Binding Sites (genetics)</term><term>Computational Biology (MeSH)</term><term>Databases, Genetic (MeSH)</term><term>Dogs (MeSH)</term><term>Gene Expression Profiling (MeSH)</term><term>Gene Expression Regulation (MeSH)</term><term>Gene Regulatory Networks (genetics)</term><term>Genome-Wide Association Study (MeSH)</term><term>Humans (MeSH)</term><term>Leishmania (physiology)</term><term>Leishmaniasis (physiopathology)</term><term>Macrophages (metabolism)</term><term>Macrophages (parasitology)</term><term>Metabolic Networks and Pathways (genetics)</term><term>Mice (MeSH)</term><term>Pan troglodytes (MeSH)</term><term>Promoter Regions, Genetic (genetics)</term><term>Rats (MeSH)</term><term>Transcription Factors (metabolism)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de profil d'expression de gènes (MeSH)</term><term>Animaux (MeSH)</term><term>Bases de données génétiques (MeSH)</term><term>Biologie informatique (MeSH)</term><term>Chiens (MeSH)</term><term>Facteurs de transcription (métabolisme)</term><term>Humains (MeSH)</term><term>Leishmania (physiologie)</term><term>Leishmaniose (physiopathologie)</term><term>Macrophages (métabolisme)</term><term>Macrophages (parasitologie)</term><term>Pan troglodytes (MeSH)</term><term>Rats (MeSH)</term><term>Régions promotrices (génétique) (génétique)</term><term>Régulation de l'expression des gènes (MeSH)</term><term>Réseaux de régulation génique (génétique)</term><term>Sites de fixation (génétique)</term><term>Souris (MeSH)</term><term>Voies et réseaux métaboliques (génétique)</term><term>Étude d'association pangénomique (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Transcription Factors</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Binding Sites</term><term>Gene Regulatory Networks</term><term>Metabolic Networks and Pathways</term><term>Promoter Regions, Genetic</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Régions promotrices (génétique)</term><term>Réseaux de régulation génique</term><term>Sites de fixation</term><term>Voies et réseaux métaboliques</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Macrophages</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Facteurs de transcription</term><term>Macrophages</term></keywords><keywords scheme="MESH" qualifier="parasitologie" xml:lang="fr"><term>Macrophages</term></keywords><keywords scheme="MESH" qualifier="parasitology" xml:lang="en"><term>Macrophages</term></keywords><keywords scheme="MESH" qualifier="physiologie" xml:lang="fr"><term>Leishmania</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Leishmania</term></keywords><keywords scheme="MESH" qualifier="physiopathologie" xml:lang="fr"><term>Leishmaniose</term></keywords><keywords scheme="MESH" qualifier="physiopathology" xml:lang="en"><term>Leishmaniasis</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Computational Biology</term><term>Databases, Genetic</term><term>Dogs</term><term>Gene Expression Profiling</term><term>Gene Expression Regulation</term><term>Genome-Wide Association Study</term><term>Humans</term><term>Mice</term><term>Pan troglodytes</term><term>Rats</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Animaux</term><term>Bases de données génétiques</term><term>Biologie informatique</term><term>Chiens</term><term>Humains</term><term>Pan troglodytes</term><term>Rats</term><term>Régulation de l'expression des gènes</term><term>Souris</term><term>Étude d'association pangénomique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The present study describes the in silico prediction of the regulatory network of Leishmania infected human macrophages. The construction of the gene regulatory network requires the identification of Transcription Factor Binding Sites (TFBSs) in the regulatory regions (promoters, enhancers) of genes that are regulated upon Leishmania infection. The promoters of human, mouse, rat, dog and chimpanzee genes were first identified in the whole genomes using available experimental data on full length cDNA sequences or deep CAGE tag data (DBTSS, FANTOM3, FANTOM4), mRNA models (ENSEMBL), or using hand annotated data (EPD, TRANSFAC). A phylogenetic footprinting analysis and a MATCH analysis of the promoter sequences were then performed to predict TFBS. Then, an SQL database that integrates all results of promoter analysis as well as other genome annotation information obtained from ENSEMBL, TRANSFAC, TRED (Transcription Regulatory Element Database), ORegAnno and the ENCODE project, was established. Finally publicly available expression data from human Leishmania infected macrophages were analyzed using the genome-wide information on predicted TFBS with the computer system ExPlain™. The gene regulatory network was constructed and activated signal transduction pathways were revealed. The Irak1 pathway was identified as a key pathway regulating gene expression changes in Leishmania infected macrophages.</div></front></TEI><affiliations><list><country><li>Tunisie</li></country><region><li>Gouvernorat de Tunis</li></region><settlement><li>Tunis</li></settlement></list><tree><noCountry><name sortKey="Benkahla, Alia" sort="Benkahla, Alia" uniqKey="Benkahla A" first="Alia" last="Benkahla">Alia Benkahla</name><name sortKey="Hornischer, Klaus" sort="Hornischer, Klaus" uniqKey="Hornischer K" first="Klaus" last="Hornischer">Klaus Hornischer</name><name sortKey="Jenhani, Ahmed Zaki" sort="Jenhani, Ahmed Zaki" uniqKey="Jenhani A" first="Ahmed-Zaki" last="Jenhani">Ahmed-Zaki Jenhani</name><name sortKey="Kel, Alexander" sort="Kel, Alexander" uniqKey="Kel A" first="Alexander" last="Kel">Alexander Kel</name><name sortKey="Konovalova, Tatiana" sort="Konovalova, Tatiana" uniqKey="Konovalova T" first="Tatiana" last="Konovalova">Tatiana Konovalova</name></noCountry><country name="Tunisie"><region name="Gouvernorat de Tunis"><name sortKey="Ghedira, Kais" sort="Ghedira, Kais" uniqKey="Ghedira K" first="Kais" last="Ghedira">Kais Ghedira</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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