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Dear Galina, Which type of identifiers do you have in your lists? You probably can use the biomaRt package to retrieve the promoter and 3'UTRs sequences. Check out the getSequence function. Once you have these sequences you could use e.g. the cosmo package search for common motifs in the sequences. Cheers, Steffen Glazko, Galina wrote: > Dear Friends, > > > > I have a list of up and down-regulated genes in rat embryos under two > different conditions, and now I would like to figure out, whether > promoters of these two groups of genes (1.up- and 2. down -regulated) > have something in common, like for example share the same transcription > factors binding sites. > > And also, I would like to know whether may be 3'UTRs in group 2 share > some microRNA targets... > > Is there Bioconductor packages to figure this out? > > > > Thank you! > > > > Best regards > > Galina > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >