What kind of data output did you get? Gene IDs & Fold Change? you could sort your genes starting off with setting a threshold for a FC of your interest, and the direction (up or down-regulation).

After this you can sort your list using some clustering online tool such as DAVID through which you can cluster your genes of interest per disease for instance - cancer.

After that you see which kind of molecule you are interested in and try to sort even further. For instance by trying protein-protein interaction with a pathway of your interest which is particularly overexpressed in your ideal setting.

Hope it helps. cheers