Network-based pathway enrichment analysis

Lu Liu, Jianhua Ruan

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    8 Scopus citations

    Abstract

    Finding out the associations between an input gene set, such as genes associated with a certain phenotype, and annotated gene sets, such as known pathways, are a very important problem in modern molecular biology. The existing approaches mainly focus on the overlap between the two, and may miss important but subtle relationships between genes. In this paper, we propose a method, NetPEA, by combining the known pathways and high-throughput networks. Our method not only considers the shared genes, but also takes the gene interactions into account. It utilizes a protein-protein interaction network and a random walk procedure to identify hidden relationships between gene sets, and uses a randomization strategy to evaluate the significance for pathways to achieve such similarity scores. Compared with the over-representation based method, our method can identify more relationships. Compared with a state of the art network-based method, EnrichNet, our method not only provides a ranked list of pathways, but also provides the statistical significant information. Importantly, through independent tests, we show that our method likely has a higher sensitivity in revealing the true casual pathways, while at the same time achieve a higher specificity. Literature review of selected results indicates that some of the novel pathways reported by our method are biologically relevant and important.

    Original languageEnglish (US)
    Title of host publicationProceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013
    Pages218-221
    Number of pages4
    DOIs
    StatePublished - 2013
    Event2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013 - Shanghai, China
    Duration: Dec 18 2013Dec 21 2013

    Publication series

    NameProceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013

    Other

    Other2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013
    CountryChina
    CityShanghai
    Period12/18/1312/21/13

    Keywords

    • enrichment analysis
    • gene sets
    • pathway
    • protein-protein interaction network
    • random walk

    ASJC Scopus subject areas

    • Biomedical Engineering

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