I thought to put this to the community:
Are there any proven ways for relating lists of genes to particular tissues, organelles, or processes? It cannot be as simply as performing enrichment against Gene Ontology or KEGG, can it? The risk of performing a basic enrichment is that you then 'cherry pick' the findings.
Another route is going the 'tissue specific' route and utilising datasets like FANTOM5 and GTEx to say that, e.g., these genes are definitively expressed in CNS or mitochondria.
Kevin
Thanks Jared. That is a good enough answer for me.