Niida, A., Smith, A. D., Imoto, S., Tsutsumi, S., Aburatani, H., Zhang, M. Q., Akiyama, T. (September 2008) Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells. BMC Bioinformatics, 9. p. 404.
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Abstract
Microarray technology has unveiled transcriptomic differences among tumors of various phenotypes, and, especially, brought great progress in molecular understanding of phenotypic diversity of breast tumors. However, compared with the massive knowledge about the transcriptome, we have surprisingly little knowledge about regulatory mechanisms underling transcriptomic diversity. RESULTS: To gain insights into the transcriptional programs that drive tumor progression, we integrated regulatory sequence data and expression profiles of breast cancer into a Bayesian Network, and searched for cis-regulatory motifs statistically associated with given histological grades and prognosis. Our analysis found that motifs bound by ELK1, E2F, NRF1 and NFY are potential regulatory motifs that positively correlate with malignant progression of breast cancer. CONCLUSION: The results suggest that these 4 motifs are principal regulatory motifs driving malignant progression of breast cancer. Our method offers a more concise description about transcriptome diversity among breast tumors with different clinical phenotypes.
| Item Type: | Paper |
|---|---|
| Subjects: | bioinformatics diseases & disorders > cancer bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > transcription diseases & disorders bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics diseases & disorders > cancer > cancer types > breast cancer diseases & disorders > cancer > cancer types |
| CSHL Authors: | |
| Communities: | CSHL labs > Zhang lab |
| Depositing User: | Matt Covey |
| Date: | 29 September 2008 |
| Date Deposited: | 26 Feb 2013 17:39 |
| Last Modified: | 26 Feb 2013 17:39 |
| PMCID: | PMC2572072 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/27552 |
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