CORE_TF: A Tool for Identifying Transcription Factor Binding Sites
Author Information
Author(s): Hestand Matthew S, van Galen Michiel, Villerius Michel P, van Ommen Gert-Jan B, den Dunnen Johan T, 't Hoen Peter AC
Primary Institution: Leiden University Medical Center
Hypothesis
Can we improve the identification of transcription factor binding sites using a novel computational tool?
Conclusion
CORE_TF successfully predicts target transcription factors and their binding sites in co-regulated genes.
Supporting Evidence
- CORE_TF was evaluated using expression and ChIP-on-chip data.
- The tool reduces false positives by matching random promoters based on GC content.
- CORE_TF outperformed existing tools like oPOSSUM and ConTra in certain aspects.
- Experimental validation confirmed the presence of predicted transcription factor binding sites.
Takeaway
CORE_TF is a computer program that helps scientists find important spots in DNA where proteins called transcription factors attach, which helps control how genes work.
Methodology
The tool uses position weight matrices and evaluates over-representation of transcription factor binding sites in experimental versus random promoter sets.
Potential Biases
Potential biases may arise from the selection of random promoters and the GC content matching process.
Limitations
The tool's performance may vary based on the quality of input data and the matching of GC content.
Statistical Information
P-Value
<0.001
Statistical Significance
p<0.05
Digital Object Identifier (DOI)
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