Where can I find verbose explanations of GO terms?

Question

[glocke01]

I have done some GO term enrichment, and I want to interpret the results. What resource(s) can I use to explain the meaning of the GO terms that I've found.

For instance, I have the term GO:0004591, whose name is, "oxoglutarate dehydrogenase (succinyl-transferring) activity." The definition at geneontology.org reads, "Catalysis of the reaction: 2-oxoglutarate + lipoamide = S-succinyldihydrolipoamide + CO2." http://amigo.geneontology.org/amigo/term/GO:0004591 (There's a link to source within the definition, but that the material at that page is even less human-readable.) I'm not familiar with any of these terms

Now, if I google "oxoglutarate dehydrogenase", I am led to Wikipedia, which informs me that there is a complex by this name involved in the citric acid cycle as well as tryptophan metabolism and lysine degradation, which seems more like biological information

The Human Metabolome Database entry for Succinyldihydrolipoamide tells me that it is a metabolite for glutamate degradation http://www.hmdb.ca/metabolites/HMDB01177.

The fact that this GO term is related to degrading/metabolizing amino acids is very interesting to me as I'm examining contaminants in protein-protein interaction assays. But I would never have known this simply by looking at the GO term.

Is there a more efficient way to gather this kind of information?

[pld]

Nope, you'll have to do the literature search.

That's kind of the point of GO enrichment, you take a very fine grained list of up/down genes and convert it into a coarse(er) grained list of functional information, which is more easily interpreted by a human.

The source on the GOC website is showing proteins annotated with that term from various databases along with the evidence used to make the annotation. GOC considers a wide range of evidence, but typically they fall into experimental/literature evidence or inferred/predicted annotations (homology with a known protein or protein family).

Answer 1

[ivivek_ngs]

You can use DAVID, ENRICHR for performing gene ontology analysis. As for the interpretation of the results I am using you want to relate the contaminants effect on PPI which you can do with the help of literature mining where you will be able to understand how the most enriched GO terms you achieved (based of FDR and ranking) have been earlier published or studied in context pf PPI (be it in human or mice). This is mostly study-centric interpretation. For more better interpretation you can construct heatmaps of GO terms if you have set of samples and try to infer the cluster of GO terms that come out for your design or create network of genes find the most relevant hub genes that are a part of the most highly ranked GO terms in your design. But for any biological interpretation you have to do a literature mining to related the context of the terms in your experimental design.

[Antonio R. Franco]

It seems that DAVID has not been updated in the last 5 years