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Gene expression and protein–protein interaction data for identification of colon cancer related genes using f-information measures

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Abstract

One of the most important and challenging problems in functional genomics is how to select the disease genes. In this regard, the paper presents a new computational method to identify disease genes. It judiciously integrates the information of gene expression profiles and shortest path analysis of protein–protein interaction networks. While the \(f\)-information based maximum relevance-maximum significance framework is used to select differentially expressed genes as disease genes using gene expression profiles, the functional protein association network is used to study the mechanism of diseases. An important finding is that some \(f\)-information measures are shown to be effective for selecting relevant and significant genes from microarray data. Extensive experimental study on colorectal cancer establishes the fact that the genes identified by the integrated method have more colorectal cancer genes than the genes identified from the gene expression profiles alone, irrespective of any gene selection algorithm. Also, these genes have greater functional similarity with the reported colorectal cancer genes than the genes identified from the gene expression profiles alone. The enrichment analysis of the obtained genes reveals to be associated with some of the important KEGG pathways. All these results indicate that the integrated method is quite promising and may become a useful tool for identifying disease genes.

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Acknowledgments

The work was done when one of the authors, S. Paul, was a Visiting Scientist of Indian Statistical Institute, Kolkata.

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Authors and Affiliations

  1. Laboratory of Systems Tumor Immunology, Department of Dermatology, University of Erlangen-Nurnberg, Erlangen, Germany

    Sushmita Paul

  2. Biomedical Imaging and Bioinformatics Lab, Machine Intelligence Unit, Indian Statistical Institute, Kolkata, 700108, India

    Pradipta Maji

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  1. Sushmita Paul
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  2. Pradipta Maji
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Correspondence to Sushmita Paul.

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Paul, S., Maji, P. Gene expression and protein–protein interaction data for identification of colon cancer related genes using f-information measures. Nat Comput 15, 449–463 (2016). https://doi.org/10.1007/s11047-015-9485-6

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