A p-Median approach for predicting drug response in tumour cells

BMC Bioinformatics

Elisabetta Fersini¹  Enza Messina¹  Francesco Archetti² 

[1] Department of Informatics, Systems and Communication, University of Milano-Bicocca, Viale Sarca, 336 Milan, Italy

[2] Consorzio Milano Ricerche, Viale Cozzi, 53 Milan, Italy

关键词: Drug response prediction;    Bayesian networks;    p-Median clustering;   

Others  :  1085380
DOI  :  10.1186/s12859-014-0353-7

 received in 2013-12-09, accepted in 2014-10-16,  发布年份 2014

【 摘 要 】

Background

The complexity of biological data related to the genetic origins of tumour cells, originates significant challenges to glean valuable knowledge that can be used to predict therapeutic responses. In order to discover a link between gene expression profiles and drug responses, a computational framework based on Consensus p-Median clustering is proposed. The main goal is to simultaneously predict (in silico) anticancer responses by extracting common patterns among tumour cell lines, selecting genes that could potentially explain the therapy outcome and finally learning a probabilistic model able to predict the therapeutic responses.

Results

The experimental investigation performed on the NCI60 dataset highlights three main findings: (1) Consensus p-Median is able to create groups of cell lines that are highly correlated both in terms of gene expression and drug response; (2) from a biological point of view, the proposed approach enables the selection of genes that are strongly involved in several cancer processes; (3) the final prediction of drug responses, built upon Consensus p-Median and the selected genes, represents a promising step for predicting potential useful drugs.

Conclusion

The proposed learning framework represents a promising approach predicting drug response in tumour cells.

【 授权许可】

   
2014 Fersini et al.; licensee BioMed Central Ltd.

【 图 表 】

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