Question: GAGE or GSEABase using expression data and pathway.gmt file for mouse
0
gravatar for snishtala03
19 months ago by
snishtala030 wrote:

Hello,

I have mouse data for 8 samples (2 conditions, 4 samples each). I performed RNA-Seq analysis and have expression data for different genes across these 8 samples. I also downloaded pathway file from http://download.baderlab.org/EM_Genesets/April_01_2017/Mouse/symbol/Mouse_AllPathways_April_01_2017_symbol.gmt

I am trying to do gene set enrichment analysis using R packages GSEABase or GAGE but the tutorial is not being very helpful for this case. moreover, since it is mouse data, I am not sure if I can use the R package to do this.

Please let me know your suggestions.

Thanks!

gage gsea rna-seq R pathway • 1.8k views
ADD COMMENTlink modified 19 months ago by bigmawen310 • written 19 months ago by snishtala030

Why would you not use gsea?

ADD REPLYlink written 19 months ago by badribio240

I need to do gene set enrichment for multiple (20) data sets. I was looking for a R option, so I can automate it and it would be faster.

ADD REPLYlink written 19 months ago by snishtala030
2
gravatar for jeff.wong
19 months ago by
jeff.wong30
jeff.wong30 wrote:

The Bader group is developing a 'Guide' to pathways and analysis.

An early beta version includes a step-by-step workflows for gene set enrichment analysis (GSEA) using RNA-Seq (http://pathwaycommons.github.io/guide/workflows/pathway_enrichment_ii/index/ ). The workflow itself provides example data; it also goes a step beyond to visualize the results of GSEA in the form of an 'Enrichment Map' (http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0013984 ) - a graphical view of the gene sets. It uses the GSEA desktop and Cytoscape software rather than R.

Please take a look. I would be particularly interested in hearing your thoughts on clarifying and improving the workflow.

ADD COMMENTlink modified 19 months ago by genomax59k • written 19 months ago by jeff.wong30

If you plan to go this route that @jeff.wong suggested, Use bader groups own curated list of gene sets, I have used it in the past and it works fine.

ADD REPLYlink written 19 months ago by badribio240

In my screen I see the letters of the workflow in a light grey which makes hard to read the workflow.

ADD REPLYlink written 19 months ago by Lluís R.780
0
gravatar for bigmawen
19 months ago by
bigmawen310
United States
bigmawen310 wrote:

Gage package has a tutorial on data preparation, which describes how to read and prepare gene set data in gmt format: http://bioconductor.org/packages/release/bioc/vignettes/gage/inst/doc/dataPrep.pdf

GAGE is a gene set/pathway analysis method, which can be applied to RNA-seq data independent of species. You need to make sure you have the gene set data and gene expression data using the same gene ID types (Entrez Gene, symbol, etc). you may generate KEGG or GO gene set data using functions kegg.gset() and go.gsets() for thousands of species in gage package. For details, check the main tutorial of gage package:
http://bioconductor.org/packages/release/bioc/html/gage.html

If you prefer a GUI tool, you may also do pathway analysis, visualization and data integration using Pathview Web server:
https://pathview.uncc.edu/

ADD COMMENTlink written 19 months ago by bigmawen310
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