Hierarchical Clustering of GO terms

Question

[The]

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.?

Answer 1

[Kevin Blighe]

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

[The]

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

[Kevin Blighe]

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.