Plant Go Term Mapping And Meaningful Visualization

Question

[K]

Hi all:

I have been involved in some medium-throughput work involving the retrieval of GO terms for a list of plant genes. This meant exploring the list of GO-tools in the NEUROLEX website (associated with the Gene Ontology project), only to find out that many tools require you to have a specific gene ID so you can retrieve the corresponding GOs. Alas, the IDs I had were not recognized by these tools (they came from a specific genome project).

An alternative I found were some tools which seem to either assign a likely ID by BLAST, or to assign the corresponding GO terms by homology via BLAST. One tool which does the first thing is the BLAST4ID tool from AgriGO; one tool which does the second thing is BLAST2GO. The first looked initially ideal; the second looked a good option... Now, the questions:

-Is it possible that the AgriGO website (my first option, I thought) has been down for almost two months? I did try some BLAST4ID jobs, but I am still expecting the results... The strange thing is, when one sends several jobs the queue seems to remain static (i.e. if I send three jobs, the length of the queue always remains the same). I have received no feedback from writing a couple of times to the people who manage AgriGO, either.

-If, as it seems, my only choice left is BLAST2GO, what remains is to be done (which I have tried) is to obtain a meaningful GO graphical representation. I have tried Revigo, but the representation seems to be prone to some randomness, and the grouping of ontologies I obtain seem to be slightly erratic at times. The BLAST2GO-generated graphics would be my last resort if no other alternatives are available. The difficulty seems to be that either I have too many GO terms, or if apply a GO-slim (Arabidopsis slim or generic plant slim -much older, if I am not wrong-) the picture becomes over-simplified. From your experience, what is a nice tool for trying to get good and meaningful visualizations of long lists of GO-terms? ¿Is there something that might I might have missed? (maybe if it is not in the NEUROLEX webpage) ¿Any further advice?

Thanks a lot in advance.

Answer 1

[vanauken]

Hi,

There is a go-friends mailing list that is a good resource for questions about tools for visualizing lists of GO terms.

Information on subscribing to the list can be found here:

http://www.geneontology.org/GO.mailing.lists.shtml

Another suggestion might be to create a customized GO slim that would allow you to visualize a broader range of ontology terms, but still not your entire list, or a subset of the ontology in which you might be particularly interested.

Good luck!

--Kimberly Van Auken Database Curator, WormBase

www.wormbase.org www.geneontology.org

[K]

Thanks, Kimberly!

I will check it out. Best regards from Spain,

Karel