Prioritizing genes associated with prostate cancer development
<p>Abstract</p> <p>Background</p> <p>The genetic control of prostate cancer development is poorly understood. Large numbers of gene-expression datasets on different aspects of prostate tumorigenesis are available. We used these data to identify and prioritize candidate...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2010-11-01
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| Series: | BMC Cancer |
| Online Access: | http://www.biomedcentral.com/1471-2407/10/599 |
| _version_ | 1831748077287899136 |
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| author | Troncoso Patricia Gorlova Olga Y Navone Nora M Maity Sankar N Zhao Hongya Sircar Kanishka Gorlov Ivan P Pettaway Curtis A Byun Jin Logothetis Christopher J |
| author_facet | Troncoso Patricia Gorlova Olga Y Navone Nora M Maity Sankar N Zhao Hongya Sircar Kanishka Gorlov Ivan P Pettaway Curtis A Byun Jin Logothetis Christopher J |
| author_sort | Troncoso Patricia |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>The genetic control of prostate cancer development is poorly understood. Large numbers of gene-expression datasets on different aspects of prostate tumorigenesis are available. We used these data to identify and prioritize candidate genes associated with the development of prostate cancer and bone metastases. Our working hypothesis was that combining meta-analyses on different but overlapping steps of prostate tumorigenesis will improve identification of genes associated with prostate cancer development.</p> <p>Methods</p> <p>A <it>Z </it>score-based meta-analysis of gene-expression data was used to identify candidate genes associated with prostate cancer development. To put together different datasets, we conducted a meta-analysis on 3 levels that follow the natural history of prostate cancer development. For experimental verification of candidates, we used in silico validation as well as in-house gene-expression data.</p> <p>Results</p> <p>Genes with experimental evidence of an association with prostate cancer development were overrepresented among our top candidates. The meta-analysis also identified a considerable number of novel candidate genes with no published evidence of a role in prostate cancer development. Functional annotation identified cytoskeleton, cell adhesion, extracellular matrix, and cell motility as the top functions associated with prostate cancer development. We identified 10 genes--<it>CDC2, CCNA2, IGF1, EGR1, SRF, CTGF, CCL2, CAV1, SMAD4</it>, and <it>AURKA</it>--that form hubs of the interaction network and therefore are likely to be primary drivers of prostate cancer development.</p> <p>Conclusions</p> <p>By using this large 3-level meta-analysis of the gene-expression data to identify candidate genes associated with prostate cancer development, we have generated a list of candidate genes that may be a useful resource for researchers studying the molecular mechanisms underlying prostate cancer development.</p> |
| first_indexed | 2024-12-21T21:44:18Z |
| format | Article |
| id | doaj.art-d8400bc9efd54f48b639d845a2e2711d |
| institution | Directory Open Access Journal |
| issn | 1471-2407 |
| language | English |
| last_indexed | 2024-12-21T21:44:18Z |
| publishDate | 2010-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Cancer |
| spelling | doaj.art-d8400bc9efd54f48b639d845a2e2711d2022-12-21T18:49:16ZengBMCBMC Cancer1471-24072010-11-0110159910.1186/1471-2407-10-599Prioritizing genes associated with prostate cancer developmentTroncoso PatriciaGorlova Olga YNavone Nora MMaity Sankar NZhao HongyaSircar KanishkaGorlov Ivan PPettaway Curtis AByun JinLogothetis Christopher J<p>Abstract</p> <p>Background</p> <p>The genetic control of prostate cancer development is poorly understood. Large numbers of gene-expression datasets on different aspects of prostate tumorigenesis are available. We used these data to identify and prioritize candidate genes associated with the development of prostate cancer and bone metastases. Our working hypothesis was that combining meta-analyses on different but overlapping steps of prostate tumorigenesis will improve identification of genes associated with prostate cancer development.</p> <p>Methods</p> <p>A <it>Z </it>score-based meta-analysis of gene-expression data was used to identify candidate genes associated with prostate cancer development. To put together different datasets, we conducted a meta-analysis on 3 levels that follow the natural history of prostate cancer development. For experimental verification of candidates, we used in silico validation as well as in-house gene-expression data.</p> <p>Results</p> <p>Genes with experimental evidence of an association with prostate cancer development were overrepresented among our top candidates. The meta-analysis also identified a considerable number of novel candidate genes with no published evidence of a role in prostate cancer development. Functional annotation identified cytoskeleton, cell adhesion, extracellular matrix, and cell motility as the top functions associated with prostate cancer development. We identified 10 genes--<it>CDC2, CCNA2, IGF1, EGR1, SRF, CTGF, CCL2, CAV1, SMAD4</it>, and <it>AURKA</it>--that form hubs of the interaction network and therefore are likely to be primary drivers of prostate cancer development.</p> <p>Conclusions</p> <p>By using this large 3-level meta-analysis of the gene-expression data to identify candidate genes associated with prostate cancer development, we have generated a list of candidate genes that may be a useful resource for researchers studying the molecular mechanisms underlying prostate cancer development.</p>http://www.biomedcentral.com/1471-2407/10/599 |
| spellingShingle | Troncoso Patricia Gorlova Olga Y Navone Nora M Maity Sankar N Zhao Hongya Sircar Kanishka Gorlov Ivan P Pettaway Curtis A Byun Jin Logothetis Christopher J Prioritizing genes associated with prostate cancer development BMC Cancer |
| title | Prioritizing genes associated with prostate cancer development |
| title_full | Prioritizing genes associated with prostate cancer development |
| title_fullStr | Prioritizing genes associated with prostate cancer development |
| title_full_unstemmed | Prioritizing genes associated with prostate cancer development |
| title_short | Prioritizing genes associated with prostate cancer development |
| title_sort | prioritizing genes associated with prostate cancer development |
| url | http://www.biomedcentral.com/1471-2407/10/599 |
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