I am interesting in identifying upstream regulators of a filtered group of transcripts, identified using either microarray or RNAseq technology.

In the past, I have used Ingenuity Pathway Analysis (IPA) from QIAGEN. IPA's Comparison Analysis uses an Upstream Regulator analytic sub-routine. This programme computes two statistical measures for each potential transcriptional regulator (TR): an overlap P-value and an activation z-score. The overlap P-value calls likely upstream regulators based on significant overlap between data set genes and known targets regulated by a TR. The activation z-score is used to infer likely activation states of upstream regulators based on comparison with a model that assigns random regulation directions.

I have also used a Cytoscape plug-in called iRegulon to identify putative upstream regulators of groups of transcripts. I know that you can interface Cytoscape with R but was wondering in there is something available to predict upstream regulators from a list of transcripts.

Thank you,  Miguel