Let's say I have a gene "A" and I want to know what is a genomic context around it in different bacterial genomes. So, I have looked around "A" in bacterial genome X, Y, Z etc. and I have pulled out a few genes that are in vicinity (both upstream and downstream) of "A" for each one of these X-Y-Z genomes.
Now, I have a list containing all these genes with their locus_tag and functional description. Based on these (and I have a lot of them), I would like to see if any specific functions are enriched around gene "A", i.e. look for clusters of orthologs (COGs) in these genes surrounding "A".
How this can be done? Initially, I wanted to use DAVID but it seems that it's main function is to look for enrichment in differentially expressed genes following RNA-seq or similar experiment. Also, my list of genes is coming from a number of various organisms.
Thank you, TP