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  • adrian
    Member
    • Oct 2009
    • 90
    #1

    integrated pathway identification

    hello group,

    What are the pathway analyses tools that can identify pathways affected given mutation, expression, methylation and copy number data, for example TCGA type data. I came across Paradigm but I am not clear if it can take all 4 data types. Thanks a lot for pointing some tools.
    Tags: None
  • bigmw
    Senior Member
    • Aug 2013
    • 124
    #2
    You may conduct pathway analysis within each data type using GAGE, then summarize the p-values using some meta-test procedure.
    To visualize the integrated datasets on pathways, you can try Pathview. It is a a tool set for pathway based data integration and visualization.

    For details please check the Bioconductor package and documentations:
    gage
    http://bioconductor.org/packages/release/bioc/html/gage.html
    GAGE is a published method for gene set (enrichment or GSEA) or pathway analysis. GAGE is generally applicable independent of microarray or RNA-Seq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity, and consistently achieves superior performance over other frequently used methods. In gage package, we provide functions for basic GAGE analysis, result processing and presentation. We have also built pipeline routines for of multiple GAGE analyses in a batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources/studies. In addition, we provide demo microarray data and commonly used gene set data based on KEGG pathways and GO terms. These funtions and data are also useful for gene set analysis using other methods.

    pathview
    http://bioconductor.org/packages/release/bioc/html/pathview.html
    Pathview is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, Pathview also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.

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