Hi Amy, The Peaks are the sites that have the greatest evidence of transcription factor binding, so these are the predicted transcription factor binding sites. You can compare the region of a particular peak of an experiment to the signal track of the same experiment in order to see a finer detail of the enrichment for the transcription factor in the region covered by the peak. The highest point of the peak, the "peak point" is the point that the corresponding signal track was the highest. ENCODE Peaks tables contain fields for statistical significance, including FDR (qValue).
Please don't hesitate to contact the mail list again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group meimeijo wrote, On 12/22/2010 11:07 PM: > Dear Vanessa, > > Thank you for the mail. > > I have another question about the peak table. > In the peak table, the position of the highest peak in a region is annotated. > Also we know that a TF might have many binding sites within the promoter > region > of a gene if it regulates the gene. > Can I have any correlation between the the position of a highest peak and > the TFBSs of the corresponding TFs? > > Sincerely yours, > Amy > > > ----- Original mail ---- > > Dear Amy, > > If you are just looking for the positions you will want to use the peaks > table: > > wgEncodeYaleChIPseqPeaksK562bYy1 > > and select the appropriate fields of interest using the table browser. > > > To answer your questions: > > The signal value (in the peaks table) is calculated using the data value (from > the signal table). > > > To find out about the statistical significance of the additional fields, > please > see the description page: > > http://genome.ucsc.edu/cgi-bin/hgTrackUi?c=chrX&g=wgEncodeYaleChIPseq > > and within this page there is a links to more detail information: > > http://genome.ucsc.edu/goldenPath/help/qValue.html > > > If you have further questions, please contact the mailing list. > > Vanessa Kirkup Swing > UCSC Genome Bioinformatics Group > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
