8.9 years ago by
Your question isn't quite clear enough. You want to compare your ChIP chip results with ANY gene expression experiment from GEO? (or some related experiment - just not done in your lab). Also, when you say "In gene expression experiments, the most expressed genes will be those that are in the top of my list...", this is confusing because gene expression experiments are typically of two varieties absolute expression levels and relative expression levels. Thus "the most expressed gene" can be viewed as either the most abundant transcript in a sample, or a gene which changes a lot under a given condition (i.e. gene expression ratios) and may or may not be very abundant. Which are you referring to?
It sounds like you want to know if your sorted list of top ChIP chip genes is enriched for top genes returned by a gene expression experiment, like looking at a venn diagram of the overlap of two lists. If that's the case you can use the hypergeometric distribution to evaluate the significance of any overlap. You have a universe of genes, you have a pool with high z-scores defined by one experiment, and you want to know if those same genes would also rank highly in another experiment. The phyper function in R would be one way to check the overlap.