I have all of my differential expression data done and I have used the Tuxedo package for all of that work. I have ~250 genes of interest and I want to identify other genes that have high expression that are transcribed in the same locus. I'm not quite sure how to move forward and if I should use cummeRbund or work with some of the cufflinks outputs or cuffdiff files. I'm working with the mouse genome. Any insight would be appreciated.