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CONFAC: automated application of comparative genomic promoter analysis to DNA microarray datasets
Suresh Karanam1, Carlos S Moreno
1Program in Bioinformatics, School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA.
Nucleic Acids Research
|June 25, 2004
Summary
We developed Conserved Transcription Factor Binding Site (CONFAC) software to identify conserved transcription factor binding sites (TFBSs) in gene regulatory regions. This tool aids comparative genomics and high-throughput gene expression analysis.
Area of Science:
- Bioinformatics
- Genomics
- Computational Biology
Background:
- Advancements in DNA microarray technology and genome sequencing enable integration of comparative genomics with gene expression analysis.
- Identifying conserved transcription factor binding sites (TFBSs) is crucial for understanding gene regulation across species.
Purpose of the Study:
- To introduce the Conserved Transcription Factor Binding Site (CONFAC) software for high-throughput identification of conserved TFBSs.
- To enable analysis of TFBSs in regulatory regions of hundreds of genes simultaneously.
Main Methods:
- CONFAC software compares non-coding regulatory sequences between human and mouse genomes.
- It identifies conserved TFBSs significantly enriched in gene promoters using a Mann-Whitney U-test.
- The software analyzes gene clusters from microarray data against control gene sets.
Main Results:
- CONFAC software enables high-throughput identification of conserved TFBSs.
- Analysis of random gene sets showed over 98% of TFBSs had false positive rates below 5%.
- Validated using four microarray studies, CONFAC identified functionally important TFBSs for each gene set.
Conclusions:
- CONFAC software is a validated tool for identifying conserved TFBSs.
- It effectively integrates comparative genomics and high-throughput gene expression data.
- The software facilitates discovery of regulatory elements critical for gene function.