Dear Bioconductor community,
except the analysis i have performed to identify potential master regulators in one microarray dataset i have analyzed, i would also like to perform some kind of TF-binding site analysis /& promoter analysis to also identify enriched TF-binding sites(which could also strengthen my results for the possible TFs i have identify) and also important cis-motifs. I have found through MsigDB (http://www.broadinstitute.org/gsea/msigdb/collections.jsp#C6) the c3: motif gene sets, which i would like to use as an input in mroast with my expressionset in similar way to ony older post i have created(https://support.bioconductor.org/p/68727/#69012). However, this time i dont want to download the complete rdata file which contains 3 different genes sets, and i intend to download the motif gene sets & the TF-gene sets to perform two separate inputs to feed for limma. Thus, as i can only download in gmt file(symbol or EntrezID), how i can convert the gmt file into an appropriate form of a list in R, in order to match with the probeIDs in my eset ?
Furthermore, there are any other web-tools to perform similar work and use as to further validate my results ??
Any help or recommendation would be essential !!!