My research group has performed this study where we have implanted a cell line derived from a melanoma brain metastasis in a patient, into a number of mice. These mice subsequently got new metastases to different organs, and we have taken samples from tumors in four different organs (brain, ovaries, adrenals, bone), three replicates from each location, and performed RNA-sequencing on them. We've also performed some exome sequencing.
Now, all that I've done so far is to attempt to find a gene signature for the metastases to the different organs, based on the gene expression. This is interesting in itself of course, but I am painfully aware that there is ever so much more that is possible to extract from the sequencing data that we have performed. The problem is that I'm very fresh in this game, and have only recently started learning how to do bioinformatics analyses. My question is whether anyone can advise me in how I can attack this data in more ways than what I've done so far? It would be much appreciated!