Affordable Access

Publisher Website

Identification of key mechanisms controlling gene expression inLeishmaniainfected macrophages using genome-wide promoter analysis

Infection Genetics and Evolution
Publication Date
DOI: 10.1016/j.meegid.2010.10.015
  • Tfs
  • Tfbss
  • Promoters
  • Phylogenetic Foot Printing
  • Orthology
  • Tsss
  • Gene Regulation
  • Chip-Seq
  • Microarray Analysis
  • Computer Science


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.

There are no comments yet on this publication. Be the first to share your thoughts.