GO enrichment of iTraq proteomic data

Question

[anish4]

Experiment

iTraq proteomic quantitation at two different conditions. The number of proteins considered reliably quantitated (after 1% FDR, at least 2 peptides) is 1765 out of 8000 proteins in the proteome. The number of proteins changed significantly is about 50. The goal is to generate a map of the enriched GO terms in this gene set.

Details

1. I am using Cytoscape with BinGO plugin to visualize GO enrichment map.
2. This is a non-model organism, so annotation is not included in the BinGO plugin. However, I have an annotation file from GO consortium and using a generic Ontology file.

Question:

1. What should be the background for my enrichment analysis? The entire 8000 genes set or the 1765 genes set.

   My assumption is the 1765 genes set. What is the suggestion of the experts?

2. If it is the 1765 genes set, how do I incorporate it in BinGO settings?

[Michael]

Please see: Looking for a tool to do GO enrichment analysis with BLAST2GO output(s) and GO enrichment in non-model organism these should provide an easy to use tool as an alternative if BinGO doesn't work. It doesn't really matter where the gene set comes from. You should use only the genes which could be measured in your experiment, the smaller set, as background, not the whole genome.