COSINE: COndition-SpecIfic sub-NEtwork identification using a global optimization method

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Abstract

Motivation: The identification of condition specific sub-networks from gene expression profiles has important biological applications, ranging from the selection of disease-related biomarkers to the discovery of pathway alterations across different phenotypes. Although many methods exist for extracting these sub-networks, very few existing approaches simultaneously consider both the differential expression of individual genes and the differential correlation of gene pairs, losing potentially valuable information in the data. Results: In this article, we propose a new method, COSINE (COndition SpecIfic sub-NEtwork), which employs a scoring function that jointly measures the condition-specific changes of both 'nodes' (individual genes) and 'edges' (gene-gene co-expression). It uses the genetic algorithm to search for the single optimal sub-network which maximizes the scoring function. We applied COSINE to both simulated datasets with various differential expression patterns, and three real datasets, one prostate cancer dataset, a second one from the across-tissue comparison of morbidly obese patients and the other from the across-population comparison of the HapMap samples. Compared with previous methods, COSINE is more powerful in identifying truly significant sub-networks of appropriate size and meaningful biological relevance. © The Author 2011. Published by Oxford University Press. All rights reserved.

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Ma, H., Schadt, E. E., Kaplan, L. M., & Zhao, H. (2011). COSINE: COndition-SpecIfic sub-NEtwork identification using a global optimization method. Bioinformatics, 27(9), 1290–1298. https://doi.org/10.1093/bioinformatics/btr136

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