Multiple Alignments of Transcription Factor Maps in Promoter Regions
Author Information
Author(s): Enrique Blanco, Roderic Guigó, Xavier Messeguer
Primary Institution: Universitat Politècnica de Catalunya
Hypothesis
Can aligning transcription factor maps instead of nucleotide sequences improve the detection of regulatory elements in gene promoters?
Conclusion
TF-map alignments can detect high-level regulatory conservation in promoter regions that typical sequence alignments miss.
Supporting Evidence
- TF-map alignments can reveal regulatory patterns that are not detectable at the sequence level.
- The method was tested on a dataset of human-mouse-chicken-zebrafish orthologous promoters.
- The study demonstrated that multiple TF-map alignments significantly reduce the number of predicted binding sites.
Takeaway
This study shows that looking at where proteins bind to DNA can help us understand how genes are controlled, even when the DNA sequences don't look similar.
Methodology
The study developed an algorithm for multiple TF-map alignments based on progressive alignment techniques.
Limitations
The lack of available collections of experimentally verified transcription factor binding sites limits the evaluation and training of the system.
Digital Object Identifier (DOI)
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