Thanks for the links of the papers although first two were not as useful to my question. I get what you mean by looking at the motif and pathway analysis based on experimental data (IPA, MetaCore, etc.) but is it still possible to do this:
Say I have two genes A and B that both regulate (not necessarily transcriptionally - it could be a number of different ways) gene C, and upstream of gene A in one tissue is a gene D. Now, based on the known experimental condition and prediction, could we make an association between gene A and B (through their both involvement with gene C) and somehow identify gene D as a "potential" regulator of gene B as well? Obviously, this will depend on tissues, but I'm just wondering whether this is possible because known computational search will not pick up gene D as a regulator of gene B because this could be conditional based on gene A. Hope that makes sense...
