I have been recently working onAffymetrix analysis on GO analysis. I am starting from 0 and I am training and learning ho to analyse these data, and have a few problem with GO analysis.
For training, I am using data from this GEO profil: http://www.ncbi.nlm.nih.gov/geoprofiles/110093622
Associated paper using these data is available and can be read on ResearchGate.
I don't have any problem (until the next time) with pre-processing data (normality/background/filtering).I have a set of 145 genes downregulated and 316 genes upregulated, which is, in my opinion, not so big for GO analysis.
The main problem is that in the related paper, they have just written (I don't have access to the supplement, I can't doublecheck) "We have performed GO analysis, and we have found that these biological processes were affected , for example Acture inflammatory response, or ECM organization". Then they selected genes in theses pathway and made a heatmap.
I have tried to use GOstat but I can't get any results. Basically what I am doing is clustering the genes in a tree, and then cutting the tree in differents groups and performing enrichment analysis on these groups, but none of my groups contains something significant. I am probably not correctly using GOstat, but this is not my main point. I am now focusing on Cytoscape with BINGO and Enrichment Map. I can get GO pathway now, but I have a lot of pathways (nothinf unusual I guess). It's possible to see for example 3-4 genes in a small pathway, such as ossification or differentiation which might interest me. However I am completely lost in front of these big networks/ edges/nodes ect.
I have never had any lectures about GO analysis and I don't really know how I should for example subgate different pathway within this list of pathway within Cytoscape ( with something else that the p-value). And I don't think that the method "Ok I have KO this gene, so I should get these differences, I am going to select pathway only related to these differences" is a good way. I have also tried GATHER and other internet tools, but it's pretty the same thing, I have let's say 100 differents pathway (with for example biological process containing 250 genes) and I don't know what to do know.
I know that this is a very broad query, but do you have any method for example, about how to analyze GO results, any tool to recommend that might help me?
Thank you and have a nice day!