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  • Francy87
    Member
    • May 2013
    • 28
    #1

    pathways differential expression analysis with KO

    Hello!
    I assigne K0 onthology to my genes from bacteria metatranscriptome. Now I'd like to carry out a differential expression analysis. Obviously, the same K0 can be involved in multiple pathways and metabolisms.
    How do you deal with this in pathway analysis? I mean, if I want to test if I have enrichment of certain pathways or metabolisms, how should I consider each gene (belonging to which pathway or metabolism)?
    sorry for the basic question, but I'm really newbie!

    Thanks
    Tags: enrichment, kegg, pathway analysis, rna sequencing
  • bigmw
    Senior Member
    • Aug 2013
    • 124
    #2
    You can use gage to do the pathway analysis and visualize the results using pathview. Both packages work with KO (KEGG Orthology) and 3000 KEGG species. For example, you may generate KO pathway gene sets using kegg.gsets function from gage. Please check out the documentation for more details:
    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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