Identification of key mechanisms controlling gene expression in Leishmania infected macrophages using genome-wide promoter analysis. - RIIP - Réseau International des Instituts Pasteur Accéder directement au contenu
Article Dans Une Revue Infection, Genetics and Evolution Année : 2011

Identification of key mechanisms controlling gene expression in Leishmania infected macrophages using genome-wide promoter analysis.

Résumé

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.

Dates et versions

pasteur-00605191 , version 1 (30-06-2011)

Identifiants

Citer

Kais Ghedira, Klaus Hornischer, Tatiana Konovalova, Ahmed-Zaki Jenhani, Alia Benkahla, et al.. Identification of key mechanisms controlling gene expression in Leishmania infected macrophages using genome-wide promoter analysis.. Infection, Genetics and Evolution, 2011, 11 (4), pp.769-77. ⟨10.1016/j.meegid.2010.10.015⟩. ⟨pasteur-00605191⟩

Collections

RIIP RIIP_TUNIS
56 Consultations
0 Téléchargements

Altmetric

Partager

Gmail Facebook X LinkedIn More