Question: Tools for functional enrichment analysis using own genome annotation
gravatar for k_mer
2.7 years ago by
k_mer0 wrote:

I am analyzing RNA-seq data for 5 different bacterial strains, 3 of which are "model" organisms (found in common databases) and 2 of which are not (e.g. not found in KEGG). I've annotated their genomes with BlastKOALA and InterProScan for KEGG and GO terms. 1) Which tools are best to use for functional enrichment analysis where I can provide my own genome annotation? 2) Ideally, for the 3 model organisms, I'd like to compare the output of the analysis for different versions of the annotations (mine vs. in existing databases).

ADD COMMENTlink modified 2.7 years ago by Jean-Karim Heriche22k • written 2.7 years ago by k_mer0
gravatar for Jean-Karim Heriche
2.7 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche22k wrote:

At its most basic, enrichment analysis is just a test for the overlap between two lists based on the hypergeometric distribution. So you could easily implement this yourself. However, a number of available tools also allow you to use custom annotations e.g. Bioconductor/R topGO, the Cytoscape plug-in BiNGO.

ADD COMMENTlink written 2.7 years ago by Jean-Karim Heriche22k
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