I have some RNA sequencing data on which I have run several pathway analyses.
I've noticed that the pathways for my wild type animals relate more strongly to cell cycling, and less strongly to immune response. By contrast, the differentially regulated pathways for my KO animals are heavily "immune" in nature.
I want to abstract from a one or even a few pathways and make the suggestion that the two differ at the level of a more fundamental process. One way to do this would be to label every pathway with a higher-order "super-pathway" like label.
Today, I've been looking into options for doing this. I went to MSig DB, but the 8 collections they have are more organizational than precise ontologies. Likewise, I found the Go Slimmer tool, but this is too high level - I would like more general than the pathway level, but more specific than the three main ontologies only.
I also looked at geneontology.org. I think the OBO and OWL files they have are a good start, and probably contain what I need. However, at the link above, I cannot find a flatfile that makes this process simple to extract the hierachical tree of ontologies, that I feel must be organized somewhere. To clarify:
For GO_0000018, there is a list of not one buy many layers of regulation to which it belongs. Is there a flat file anywhere that makes parsing this easy? Or what would be the recommendation for doing it?
Finally, if I have additional pathways from KEGG, GO, Biocarta, MSigDB, and other sources, is it recommended to use their GO external tool? Or how should I approach this problem if I have pathways curated from many sources? Thank you.
EDIT: Another way to ask the above question would be: is there a simple way to download a file that stores all the information necessary to create this drill-down tool: http://amigo.geneontology.org/amigo/dd_browse. Or, is this information scattered across many files?