Hello,
So, I've tried PantherDB for my gene ontology analysis tools. I tried it to get pathway that included in my interesting genes set. What I get is quietly good but I have a bit hard to understand it. My question is:
I get the percentage of genes that included in a pathway. The percentage is compared to the all genes that I've submitted and the genes that successfully mapped. How do I get the percentage for only in that pathway? What I mean is, in a pathway, there are many genes involved. I want to know the significance level of the genes found in my gene sets that is mapped to those pathways. For example, a pathway consist of 20 genes and from my list, I mapped 10 of them. It should be 50% of that pathway right? On the other hand, if I have 50 genes from a pathway which has 200 genes, I will only get 25%. From the result of PantherDB, the pathway which I have 50 genes would have bigger percentage compare to the pathway which I have only 10 genes. The fact that the only 10 genes cover 50% of the original pathway can not be seen from the percentage result of PantherDB. Is there any tools out there which can give me this kind of analysis?
I am not familiar with pathway analysis tools, but I know you can do such analysis in R. For example 'graphite' is an R-package consists of pathways and genes included in them.
Thank you for your suggestion. I will check that one.