Identifying novel prostate cancer associated pathways based on integrative microarray data analysis

Wang, Ying, Chen, Jiajia, Li, Qinghui, Wang, Haiyun, Liu, Ganqiang, Jing, Qing and Shen, Bairong (2011) Identifying novel prostate cancer associated pathways based on integrative microarray data analysis. Computational Biology and Chemistry, 35 3: 151-158. doi:10.1016/j.compbiolchem.2011.04.003

Author Wang, Ying
Chen, Jiajia
Li, Qinghui
Wang, Haiyun
Liu, Ganqiang
Jing, Qing
Shen, Bairong
Title Identifying novel prostate cancer associated pathways based on integrative microarray data analysis
Journal name Computational Biology and Chemistry   Check publisher's open access policy
ISSN 1476-9271
Publication date 2011-06
Sub-type Article (original research)
DOI 10.1016/j.compbiolchem.2011.04.003
Volume 35
Issue 3
Start page 151
End page 158
Total pages 8
Place of publication Oxford, United Kingdom
Publisher Elsevier
Collection year 2012
Language eng
Abstract The development and diverse application of microarray and next generation sequencing technologies has made the meta-analysis widely used in expression data analysis. Although it is commonly accepted that pathway, network and systemic level approaches are more reproducible than reductionism analyses, the meta-analysis of prostate cancer associated molecular signatures at the pathway level remains unexplored. In this article, we performed a meta-analysis of 10 prostate cancer microarray expression datasets to identify the common signatures at both the gene and pathway levels. As the enrichment analysis result of GeneGo's database and KEGG database, 97.8% and 66.7% of the signatures show higher similarity at pathway level than that at gene level, respectively. Analysis by using gene set enrichment analysis (GSEA) method also supported the hypothesis. Further analysis of PubMed citations verified that 207 out of 490 (42%) pathways from GeneGo and 48 out of 74 (65%) pathways from KEGG were related to prostate cancer. An overlap of 15 enriched pathways was observed in at least eight datasets. Eight of these pathways were first described as being associated with prostate cancer. In particular, endothelin-1/EDNRA transactivation of the EGFR pathway was found to be overlapped in nine datasets. The putative novel prostate cancer related pathways identified in this paper were indirectly supported by PubMed citations and would provide essential information for further development of network biomarkers and individualized therapy strategy for prostate cancer.
Keyword Meta-analysis
Pathway enrichment analysis
GeneGo database
KEGG database
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2012 Collection
Institute for Molecular Bioscience - Publications
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