Is there a way to organize or cluster a list of Goterms.

Question

[ahdee]

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

Answer 1

[Jean-Karim Heriche]

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.