Software

TF Target Mapper: A BLAST search tool for the identification of Transcription Factor target genes

Sebastiaan Horsman^1,2 , Michael J Moorhouse^2,4 , Victor CL de Jager^2,5 , Peter van der Spek² , Frank Grosveld¹ , John Strouboulis¹ and Eleni Z Katsantoni^1,3

¹  Department of Cell Biology, Erasmus Medical Center, Dr Molewaterplein 50, 3015GE Rotterdam, The Netherlands

²  Department of Bioinformatics, Erasmus Medical Center, Dr Molewaterplein 50, 3015GE Rotterdam, The Netherlands

³  Foundation for Biomedical Research of the Academy of Athens, Hematology Laboratory, Soranou tou Ephessiou 4, 115.27 Athens, Greece

⁴  Present address : Department of Virology, Erasmus Medical Center, Dr Molewaterplein 50, 3015GE Rotterdam, The Netherlands

⁵  Present address : NBIC, Toernooiveld 1, 6525 ED, Nijmegen, The Netherlands

author email corresponding author email

BMC Bioinformatics 2006, 7:120doi:10.1186/1471-2105-7-120

Published:	8 March 2006

Abstract

Background

In the current era of high throughput genomics a major challenge is the genome-wide identification of target genes for specific transcription factors. Chromatin immunoprecipitation (ChIP) allows the isolation of in vivo binding sites of transcription factors and provides a powerful tool for examining gene regulation. Crosslinked chromatin is immunoprecipitated with antibodies against specific transcription factors, thus enriching for sequences bound in vivo by these factors in the immunoprecipitated DNA. Cloning and sequencing the immunoprecipitated sequences allows identification of transcription factor target genes. Routinely, thousands of such sequenced clones are used in BLAST searches to map their exact location in the genome and the genes located in the vicinity. These genes represent potential targets of the transcription factor of interest. Such bioinformatics analysis is very laborious if performed manually and for this reason there is a need for developing bioinformatic tools to automate and facilitate it.

Results

In order to facilitate this analysis we generated TF Target Mapper (Transcription Factor Target Mapper). TF Target Mapper is a BLAST search tool allowing rapid extraction of annotated information on genes around each hit. It combines sequence cleaning/filtering, pattern searching and BLAST searches with extraction of information on genes located around each BLAST hit and comparisons of the output list of genes or gene ontology IDs with user-implemented lists. We successfully applied and tested TF Target Mapper to analyse sequences bound in vivo by the transcription factor GATA-1. We show that TF Target Mapper efficiently extracted information on genes around ChIPed sequences, thus identifying known (e.g. α-globin and ζ-globin) and potentially novel GATA-1 gene targets.

Conclusion

TF Target Mapper is a very efficient BLAST search tool that allows the rapid extraction of annotated information on the genes around each hit. It can contribute to the comprehensive bioinformatic transcriptome/regulome analysis, by providing insight into the mechanisms of action of specific transcription factors, thus helping to elucidate the pathways these factors regulate.