Inferring gene dependency network specific to phenotypic alteration based on gene expression data and clinical information of breast cancer.

ABSTRACT: Although many methods have been proposed to reconstruct gene regulatory network, most of them, when applied in the sample-based data, can not reveal the gene regulatory relations underlying the phenotypic change (e.g. normal versus cancer). In this paper, we adopt phenotype as a variable when constructing the gene regulatory network, while former researches either neglected it or only used it to select the differentially expressed genes as the inputs to construct the gene regulatory network. To be specific, we integrate phenotype information with gene expression data to identify the gene dependency pairs by using the method of conditional mutual information. A gene dependency pair (A,B) means that the influence of gene A on the phenotype depends on gene B. All identified gene dependency pa

SUBMITTER: Zhou X 

PROVIDER: S-EPMC3956890 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature