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Generation of p53 target database via integration of microarray and global p53 DNA-binding site analysis
Suxing Liu1, Asra Mirza, Luquan Wang
1Tumor Biology Department, Schering-Plough Research Institute, Kenilworth, NJ, USA.
Methods in Molecular Biology (Clifton, N.J.)
|June 29, 2004
Summary
Researchers developed a novel strategy to identify genes regulated by transcription factors, like p53, using genomic data and microarray analysis. This approach enhances understanding of gene regulatory networks and aids in discovering new signaling pathways.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- The human genome sequence and cDNA microarray technology offer new avenues for studying cellular regulation.
- Identifying genes directly controlled by specific transcription factors is crucial for understanding cellular mechanisms.
Purpose of the Study:
- To present a strategy for identifying genes regulated by transcription factors, specifically p53, in the human genome.
- To create a database of potential p53 target genes and validate these findings.
Main Methods:
- Collected gene regulatory sequences (promoters/introns) using GenBank and transcript maps.
- Utilized the 'FindPatterns' program to identify p53 DNA-binding sequences in regulatory regions.
- Employed cDNA microarray, Taqman analysis, and chromatin immunoprecipitation for validation and genomic-scale analysis.
Main Results:
- Developed the p53 Target Database, containing human genes with p53-binding sites in their regulatory regions.
- Validated in silico predictions and microarray data, confirming enrichment of transcriptionally regulated genes by p53.
- Identified potential signaling pathways connected to p53.
Conclusions:
- The integrated approach of genomic data and gene expression analysis provides a novel method for studying global gene regulatory networks.
- This strategy effectively enriches for direct transcription factor targets and can be extended to other transcription factors.