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BMC Bioinformatics

, 9:S16

First Online: 28 May 2008


BackgroundGene pathway can be defined as a group of genes that interact with each other to perform some biological processes. Along with the efforts to identify the individual genes that play vital roles in a particular disease, there is a growing interest in identifying the roles of gene pathways in such diseases.

ResultsThis paper proposes an innovative fuzzy-set-theory-based approach, Multi-dimensional Cluster Misclassification test MCM-test, to measure the significance of gene pathways in a particular disease. Experiments have been conducted on both synthetic data and real world data. Results on published diabetes gene expression dataset and a list of predefined pathways from KEGG identified OXPHOS pathway involved in oxidative phosphorylation in mitochondria and other mitochondrial related pathways to be deregulated in diabetes patients. Our results support the previously supported notion that mitochondrial dysfunction is an important event in insulin resistance and type-2 diabetes.

ConclusionOur experiments results suggest that MCM-test can be successfully used in pathway level differential analysis of gene expression datasets. This approach also provides a new solution to the general problem of measuring the difference between two groups of data, which is one of the most essential problems in most areas of research.

List of abbreviationsMCM-testmulti-dimensional Cluster Misclassification test

CM-testcluster misclassification test

FM-testfuzzy membership test

GSEAgene set enrichment analysis

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Autor: Lily R Liang - Vinay Mandal - Yi Lu - Deepak Kumar


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