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Correlating protein-DNA and protein-protein interaction networks
Thomas Manke1, Ricardo Bringas, Martin Vingron
1Max-Planck-Institute for Molecular Genetics, Abt Bioinformatik, Ihnestr. 73, 14195 Berlin, Germany.
Journal of Molecular Biology
|October 1, 2003
Summary
We identified co-occurring transcription factor (TF) modules in yeast, revealing new gene functions. TF binding site co-occurrence correlates with protein interaction networks, suggesting functional relationships.
Area of Science:
- Molecular Biology
- Systems Biology
- Genomics
Background:
- Transcription factors (TFs) regulate gene expression by binding to specific DNA sequences.
- Understanding TF co-occurrence is crucial for deciphering complex gene regulatory networks.
Purpose of the Study:
- To identify prevalent pairs and higher-order tuples of co-occurring transcription factors (TFs) in Saccharomyces cerevisiae.
- To explore the relationship between TF binding site co-occurrence and protein-protein interactions.
Main Methods:
- Analysis of genome-wide protein-DNA binding data in yeast.
- Utilizing large-scale protein interaction data.
- Investigating the correlation between TF binding site proximity and protein interaction network vicinity.
Main Results:
- Identified several biologically meaningful TF modules, enabling putative annotation of unclassified genes.
- Discovered new target genes for the Mcm1-Fkh2-Ndd1 module involved in cell-cycle control and filament formation.
- Demonstrated a significant correlation between TF binding site co-occurrence and proximity in the protein interaction network.
Conclusions:
- Co-occurring TF binding sites suggest functional relationships and regulatory modules.
- Directly interacting TFs and those in protein complexes are more likely to co-occur.
- This approach aids in understanding gene regulation and annotating novel gene functions.