TF Target Mapper: A Tool for Identifying Gene Targets of Transcription Factors
Author Information
Author(s): Sebastiaan Horsman, Michael J. Moorhouse, Victor C.L. de Jager, Peter van der Spek, Frank Grosveld, John Strouboulis, Eleni Z. Katsantoni
Primary Institution: Erasmus Medical Center
Hypothesis
Can we automate the identification of transcription factor target genes using bioinformatics tools?
Conclusion
TF Target Mapper is an efficient tool for extracting information on genes around transcription factor binding sites.
Supporting Evidence
- TF Target Mapper was tested with 95 sequences and identified 372 genes in 27 minutes.
- The tool successfully identified known targets of GATA-1, such as α-globin and ζ-globin.
- Preliminary data showed that most sequences analyzed were enriched in GATA-1 immunoprecipitated material.
Takeaway
TF Target Mapper helps scientists quickly find genes that are controlled by specific proteins in the DNA.
Methodology
The tool uses BLAST searches to analyze sequences bound by transcription factors and extract gene information.
Potential Biases
ChIP assays can result in high background due to non-specific binding of DNA.
Limitations
The tool was mainly tested on the mouse genome and may require adjustments for other genomes.
Digital Object Identifier (DOI)
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