Finally I have my list of overexpressed genes. My next step is try to understand the biological context of these genes.
I am working with a well annotated organism Drosophila melanogaster, so there are many tools to interpreting this data. One of this is the enrichment of GeneOntology in which I only submit my list of gene id and this tool do the enrichment and plots. However I have noticed that not all genes in my list are in the final plot, so if I only use this plot possibily I will be ignoring some genes that could be important.
What can I do,?
What tools do you use to represent your over and down expressed genes?
What exactly is your scientific question that you want to answer with your anlysis?