When doing enrichment analysis using public pathways databases (e.g. KEGG, Reactome) or ontologies (e.g. Gene Ontology, Human Phenotype Ontology) I often get categories, which contain both up and down-regulated genes according to the gene expression data. I interpret it as potential indicator that some process is "disrupted" or that my data might resemble particular phenotype. However, I noticed that people are rather interested in up- or down-regulated processes and they tend to equate it with enriched category having up- or down-regulated genes only. I think such understanding might not reflect how the biological processes work (as they can have both repressed and activated genes at the same time), so I seek answers for the following questions:
- How do you interpret enriched categories having both up- and down-regulated genes? Do you perform enrichment analysis on the whole set of differentially expressed genes (I saw practices when people separate up- and down- genes)?
- Do you know any bioinformatics tools or algorithms that go deeper in functional/ontology enrichment analysis and try to tell if the particular biological process is indeed (de)activated (by inferring the state of the final products of the pathway, for example).
Thanks in advance.