Finding DNA Motifs in Mammalian Gene Expression Data
Author Information
Author(s): Huber Bertrand R, Bulyk Martha L
Primary Institution: Brigham and Women's Hospital and Harvard Medical School
Hypothesis
Many orthologous genes expressed in a similarly tissue-specific manner in human and mouse are likely to be co-regulated by orthologous transcription factors through similar cis regulatory regions.
Conclusion
The integration of results from multiple motif finding tools identifies and ranks more known and novel motifs than using just one tool.
Supporting Evidence
- The study discovered both previously known and many novel candidate regulatory DNA motifs in all 18 tissue-specific expression clusters examined.
- If a transcription factor was expressed in the specified tissue, a matching motif was often identified.
- The method used allowed for the integration of results from multiple motif finding tools.
Takeaway
Scientists looked for patterns in DNA that help control how genes are turned on or off in different tissues, and they found many new patterns that could help us understand gene regulation better.
Methodology
Automated motif searching and merging across four different motif finding algorithms, followed by filtering of the resulting motifs.
Limitations
The study focused only on 1 kb upstream regions and may miss motifs located further away from the transcription start sites.
Digital Object Identifier (DOI)
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