Hi Diego, Jim Kent, who worked on this, had these comments on Cluster Score:
" The cluster score is the max score for that transcription factor for any cell line where the transcription factor was ChIP-seq'd. The score varies from 0-1000, and reflects the strength of the ChIP-seq signal. This signal is generally a reflection of how often the transcription factor occupies the region inside of the cluster. This occupancy level is determined in part by the affinity of the transcription factor for the DNA in the cluster, especially for transcription factors that bind DNA directly. In this case, in truth, the transcription factor is probably binding to one or more smaller binding sites within the cluster, but the ChIP-seq assay is not precise enough to get it down to the actual binding site. However, for most transcription factors, there's substantial binding that occurs indirectly, via other factors, as well as direct binding. The level of binding observed is modulated by the openness of the chromatin as well. Even a perfect match to the transcription factor's favorite DNA sequence may not be well occupied if it is in a region of closed chromatin. Also the cluster won't be occupied in cells where the transcription factor itself is not present at reasonable levels. So, the whole thing is a little complex, but in general, the higher the number here, the more likely you are to see the associated transcription factor someplace in the nearby vicinity." Please let us know if you have any additional questions: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 10/13/11 5:58 PM, Hoyle, Diego wrote: > Cordial regards, > > > > My name is Diego Hoyle, and I am a student preparing to go into graduate > school. I saw that I can post questions about UCSC Genome Browser in this > way, so I decided to submit my question. > > > > I am searching for transcription factor binding sites and enhancer binding > sites that could potentially affect the level of expression of the > RP5-1099E6.3 transcript. Using UCSC Genome Browser, I was able to find some > transcription factor binding sites inferred from ChIP-seq data; however, I am > having a little bit of trouble interpreting the data. > > > > Using a specific example, on the Web Page: > > http://genome.ucsc.edu/cgi-bin/hgc?hgsid=217526537&o=216367187&t=216367637&g=wgEncodeRegTfbsClustered&i=KAP1 > > > > The Cluster Score is given. My questions are as follows: First, I would like > to know whether the Cluster Score includes the affinity of the transcription > factor for that particular site. If it does, then I would like to know if > there is a way for me to estimate whether a certain cluster score would > indicate a reasonably high affinity of the transcription factor for the > particular site such that I could consider that transcription factor as a > potential candidate regulator of my transcript of interest in a given cell > type. > > > > Thank you for your time and help, and I will be looking forward to your reply. > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
