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
