Related Experiment Videos
Condition specific transcription factor binding site characterization in Saccharomyces cerevisiae
Rhonda Harrison1, Charles DeLisi
1Bioinformatics Department, Boston University, 44 Cummington Street, Boston, MA 02215, USA. rhonda@bu.edu
Bioinformatics (Oxford, England)
|October 12, 2002
Summary
This study introduces a computational method to identify transcription factor binding sites using genome-wide data. The approach refines motif discovery for more accurate identification of regulatory elements.
Area of Science:
- Computational Biology
- Genomics
- Bioinformatics
Background:
- Transcription factor binding sites (TFBS) regulate gene expression.
- Identifying TFBS is crucial for understanding gene regulation.
- Current methods for TFBS identification have limitations.
Purpose of the Study:
- To develop a computational process for elucidating transcription factor binding sites.
- To identify promoter regions using genome-wide expression and binding profiles.
- To establish a more accurate motif discovery protocol.
Main Methods:
- Utilizing genome-wide expression and binding profiles.
- Locally aligning intergenic sequences to generate anchor motifs.
- Incorporating variability within motifs for enhanced accuracy.
Main Results:
- A computational process for TFBS elucidation is demonstrated.
- Potentially more accurate motifs are generated by accounting for variability.
- A measure of motif quality based on binding site occurrence is presented.
Conclusions:
- The developed method refines transcription factor binding site identification.
- The approach offers greater control and accuracy compared to existing protocols.
- The IGRDB database and associated datasets are publicly available.