Hi Jim, The darkness of the box is proportional to the maximum signal strength observed in any cell line. The score (between 0-1000) is what determines how darkly the item is displayed (with 1000 being black).
You would have to contact the authors to find out exactly how they calculated the signal strength. There are several links to authors' labs in the credits section here: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegTfbsClustered If you have any additional questions, please reply to: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 3/12/12 3:30 AM, Jim Liu wrote: > Hi Steve, > > Thank you for the reply. > In UCSC page, the explanation is as follows: > A gray box encompasses the peaks of transcription factor occupancy. > The darkness of the box is proportional to the maximum signal strength > observed in any cell line. > > However, it didn't tell us that how the darkness of the box proportion > to the signal strength. In addition, can you tell us how the authors > calculate the signal strength? > > Thank you. > > Jim > > > On Fri, Mar 9, 2012 at 3:13 AM, Steve Heitner<[email protected]> wrote: >> Hello. >> >> I apologize - I don't believe the answer I provided earlier answered the >> specific question you were asking. In tracks whose items are displayed in >> grayscale, the score (between 0-1000) is what determines how darkly the item >> is displayed (with 1000 being black). The score is not part of the raw data >> used to generate the track but rather is a quantification that summarizes >> the cluster of data found at that genomic location. >> >> Please see the Display Conventions section of the description page of this >> track for a detailed explanation: >> >> http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegTfbsClustered >> >> Please contact us again at [email protected] if you have any further >> questions. >> >> --- >> Steve Heitner >> UCSC Genome Bioinformatics Group >> >> -----Original Message----- >> From: [email protected] [mailto:[email protected]] On >> Behalf Of Steve Heitner >> Sent: Wednesday, March 07, 2012 11:59 AM >> To: 'Chun-Chi Jim Liu'; [email protected] >> Cc: 'Hsuan-Yu Chen' >> Subject: Re: [Genome] Could you tell me the definition of score in >> wgEncodeRegTfbsClustered table? >> >> Hello. >> >> I would suggest looking at the journal article by Euskirchen et al. >> referenced on the ENC TF Binding supertrack page: >> http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeTfBindingSuper. >> >> If this does not answer your question, I would try contacting the authors of >> that paper who are listed in the Credits section of the Transcription Factor >> ChIP-seq description page. >> >> Please contact us again at [email protected] if you have any further >> questions. >> >> --- >> Steve Heitner >> UCSC Genome Bioinformatics Group >> >> -----Original Message----- >> From: [email protected] [mailto:[email protected]] On >> Behalf Of Chun-Chi Jim Liu >> Sent: Tuesday, March 06, 2012 11:34 PM >> To: [email protected] >> Cc: 'Hsuan-Yu Chen' >> Subject: [Genome] Could you tell me the definition of score in >> wgEncodeRegTfbsClustered table? >> >> Hi! >> >> >> >> Could you tell me the definition of score in wgEncodeRegTfbsClustered table? >> >> See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=246255005 >> <http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=246255005&c=chr1&g=wgEncodeR >> egTfbsClustered> &c=chr1&g=wgEncodeRegTfbsClustered >> >> >> >> Best regards, >> >> >> >> Chun-Chi Jim Liu >> >> Institute of Genomics and Bioinformatics >> >> National Chung Hsing University >> >> >> >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
