Hello All,
I wish to know how I can cluster hierarchically gene Ontology terms for the following type of data. I have GO (BP) terms enriched from two experiments (CondA and CondB). The values are -log10 P-values for the term enrichment . I wish to (hierachically) cluster the table along the rows i.e by the GO terms.
Can anybody suggest some code/packages etc.?
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I technically do it here, but this is a messy tutorial, by my [high] standards: Clustering of DAVID gene enrichment results from gene expression studies
There is also ClueGO, available in Cytoscape: http://apps.cytoscape.org/apps/cluego
Then there is also REVIGO: http://revigo.irb.hr/
Kevin
Thanks Kevin,
I'll definitely try the tools you've suggested and I've used Revigo before. Have you used goSTAG ? If so, any comments on its functionalities and usefulness ?
https://bioconductor.org/packages/release/bioc/vignettes/goSTAG/inst/doc/goSTAG.html
-A
Hi, I have never heard of goSTAG, but it seems that every acronym that is possible with the letters 'GO' will eventually be used for programs that perform gene-set enrichment via Gene Ontology.
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