...

Starting with a region list, you may detect either known or de novo motifs using the ChIP-Seq
workflow if your spreadsheet has been associated with a species and a reference genome as
described in the import section.Set Workflows to

• Select ChIP-

...

• Seq from the Workflows drop-down menu
• Select Motif detection from the Peak Analysis section of the workflow

...

Both options
(Discover de novo motifs and Search for known motifs) can now be performed
. Motifs (de novo) may be displayed in the Genome Browser and known detected motifs may be
viewed in web-log format by right-clicking on a header row of the motif spreadsheet.

Determining the average values for a region list

If you have a region list or a bed file and you have a microarray experiment with data, you can summarize the data according to the genomic coordinates contained in the region list. For instance, the region list contains a list of CpG islands, the experiment contains methylation percentage values for probes (β values), and you would like to summarize the methylation values for individual probes for the CpG islands. Or you have a list of copy number amplifications, microarray gene expression data, and you are interested in determining if the average intensities of the probes in those regions is higher than expected.