I was wondering if anyone could guide me in regards to gene ontology analysis using DAVID 6.8. I have a secretomics data output between two experimental groups (without treatment: control and with treatment). A number of genes/proteins are significantly increased in the treatment group compared with control, while another group are downregulated.
I wondered if it made sense to analyse the gene ontologies separately in DAVID to find biological processes that differ in the "upregulated" and "downregulated" scenarios? I came across one paper which certainly affirmed this is the better thing to do. Reference: Hong, G., W. Zhang, H. Li, X. Shen, and Z. Guo, Separate enrichment analysis of pathways for up- and downregulated genes. J R Soc Interface, 2014. 11(92): p. 20130950. Is there any value in trying to incorporate the z-scores from the original data into the analysis or is this impossible? It seems that GO analysis may be limited to the gene set rather than the quantitative differences between the sets of genes between experimental and control groups.
Anyone have any thoughts on this?