pathways differential expression analysis with KO

Francy87

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Join Date: May 2013

Posts: 28
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#1

pathways differential expression analysis with KO

11-18-2014, 11:23 AM

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

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Join Date: Aug 2013

Posts: 124
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#2

12-03-2014, 05:44 PM

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.

http://bioconductor.org/packages/release/bioc/html/pathview.html
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