This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Is there a way to organize or cluster a list of Goterms.

Hi, if I have a list of GO terms generated from a program, say Panther, for example:

CHROMOSOME_ORGANIZATION_AND_BIOGENESIS      GO:0051276
CHROMATIN_MODIFICATION                      GO:0016568
LEUKOCYTE_ACTIVATION                        GO:0045321
LYMPHOCYTE_ACTIVATION                       GO:0046649

Is there any program that I use to take the above goterms and organize/cluster into some sort of hierarchical tree and/or table? Would be nice if I give the above table and the program recognizes that the above 2 rows are chromosomal organizer and bottom two are immune response.

Thanks

go-terms amigo microarray rna-seq
• 2,160 views • link
updated by Ram Ram • written by ahdee • ahdee

1 answer

You can compute semantic similarity measures between terms then cluster the terms using the resulting similarity matrix. There are various R packages to compute semantic similarities, e.g. GOSemSim.

• 0 views • link
updated by Ram Ram • written by Jean-Karim Heriche Jean-Karim Heriche

Log in to answer this question.

More posts like this