Hierarchical Clustering of GO terms
1
0
Entering edit mode
3 months ago
The ▴ 160

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.?

enter image description here

Clustering GO similarity Ontology • 433 views
ADD COMMENT
4
Entering edit mode
3 months ago

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

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 2175 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6