Question: Enrichment Analysis from DESeq2 data
gravatar for gkuffel22
2.7 years ago by
United States
gkuffel2270 wrote:

Hi everyone,

I use DESeq2 for all of my RNA-Seq analysis. Can anyone recommend a tool that works seamlessly with DESeq2 data to perform enrichment analysis? Thanks everyone.

rna-seq deseq2 • 2.4k views
ADD COMMENTlink modified 2.7 years ago by EagleEye6.6k • written 2.7 years ago by gkuffel2270

Hello gkuffel22!

It appears that your post has been cross-posted to another site:

This is typically not recommended as it runs the risk of annoying people in both communities.

ADD REPLYlink written 2.7 years ago by WouterDeCoster43k
gravatar for arnstrm
2.7 years ago by
Ames, IA
arnstrm1.8k wrote:

If you have a list of genes that are deferentially expressed, you can run enrichment analysis (not just DESeq results). I use ontologizer, which is a command line tool and very easy to run. Here is how to run:

  1. Before you begin, you need to have 2 important files. 1. GO ontology file, where you describe every possible GO term numbers with what they are. You can easily get this from here: 2. Mapping file, this will describe the association of genes of the organism with GO terms (also available on GO website, if it is a well known organism, else you may have to generate your own).

  2. Once you have these 2 files, you can run Ontologizer

    java -jar Ontologizer.jar -a association.anno -g gene_ontology.obo -s your_input_list.txt -p population.txt -c Parent-Child-Union -m Westfall-Young-Single-Step -d 0.05 -r 1000

    Here the population.txt is basically the full list of genes that you have in anno file. The only time you need to change this is when you have a different background set to test. You can also play around the other settings like --mode, --resamplingsteps to optimize. With the -d it will also generate a dot file, that can be used with GraphViz to show the pathway where these genes are enriched.

  3. To generate graphs:

    dot -Tpng -o output.png

Hope this helps! (you can also run BiNGO, a cytoscape plugin which is easier if you are new to command line!)

ADD COMMENTlink written 2.7 years ago by arnstrm1.8k
gravatar for moxu
2.7 years ago by
moxu450 wrote:

I use GSEA (Broad Institute). Just rank your genes by -log(P-value) * sign(logFC).

ADD COMMENTlink written 2.7 years ago by moxu450

why use this value instead of log2FC?

ADD REPLYlink written 2.3 years ago by langya60

log2FC is not stable, lower p-value is more stable. I would weigh true signal more than big signal. My personal experience also supports this view. Actually, ranking by -log(P-value) * sign(logFC) is identical to ranking by signal-to-noise ratio.

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by moxu450
gravatar for EagleEye
2.7 years ago by
EagleEye6.6k wrote:

GeneSCF for your significantly differentially expressed genes (gene symbols or ids) from DESeq2.

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by EagleEye6.6k
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