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

doi:10.1186/1471-2105-7-120

BMC Bioinformatics

Volume 7

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Horsman S
Moorhouse MJ
de Jager VC
van der Spek P
Grosveld F
Strouboulis J
Katsantoni EZ

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de Jager VC
van der Spek P
Grosveld F
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Katsantoni EZ
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TF Target Mapper: A BLAST search tool for the identification of Transcription Factor target genes

Sebastiaan Horsman¹^,2 , Michael J Moorhouse²^,4 , Victor CL de Jager²^,5 , Peter van der Spek² , Frank Grosveld¹ , John Strouboulis¹ and Eleni Z Katsantoni¹^,3

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

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

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

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

⁵Present 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

Additional files

Additional File 1:

TF Target Mapper application analytical flowchart : Analytical flowchart of the TF Target Mapper application including all its functions (RE: Restriction Endonuclease, TF: Transcription Factor).

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Additional File 3:

Chromatin immunoprecipitation (ChIP) : Description of the ChIP method.

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Additional File 2:

Chromatin immunoprecipitation (ChIP) to confirm sequences analysed as GATA-1 targets : Chromatin immunoprecipitation (ChIP) experiments with GATA-1 antibodies to confirm sequences analyzed by TF Target Mapper as GATA-1 targets. Semi-quantitative PCR was used with primers specific for sequences that were found by TF Target Mapper analysis to contain binding sites for hematopoietic transcription factors. The control experiments refer to ChIP performed with rat IgG, whereas GATA-1 ChIP assays were performed with the GATA-1 N6 rat monoclonal antibody. Input refers to DNA from formaldehyde crosslinked sonicated chromatin. It can be seen that most of the sequences tested (with the only exception of the sequence G) were enriched by the GATA-1 antibody compared to the control. The chromosomes where the sequences map are also depicted (chr: chromosome).

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