About transcription factor ChIP-seq from ENCODE with Factorbook Motifs
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Yuchen Feng
Oct 12, 2017, 11:18:42 AM10/12/17
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Hello sir or madam:
I am a PhD student of University of Newcastle. I try to use transcription factor ChIP-seq from ENCODE with Factorbook Motifs to find out potential transcription factor on the promoter region of one gene, but I have some problems to understand those gray or black bars. Does the length of bars represent the length of base pair fragment ChIP-seq showed? And website mentions the darkness of bars refers to signal strength. What's the meaning of signal? On top of that, after getting sequence of each fragment, did you use Factorbook to search the concensus binding site of each transcription factor? Bars without green highlight means you didn't find concensus binding site using Factorbook. Is that right? Thank you for your help and I am looking forward to your reply.
Best regards
Yuchen
PhD candidate, Biomedical and Pharmacy
Melanoma Research Laboratory
LS3-20, Life Sciences Building
University of Newcastle
NSW 2308, Australia
Cath Tyner
Oct 12, 2017, 6:10:08 PM10/12/17
to Yuchen Feng, gen...@soe.ucsc.edu
Hello Yuchen,
Thank you for contacting the UCSC Genome Browser support team and inquiring about the details of ENCODE Txn Factor ChIP track.
To read about details for this track, you can view the ENCODE Txn Factor ChIP track description page.
Additional views of the underlying ChIP-seq data and documentation on the methods used to generate it are available from the ENCODE Uniform TFBS track (this track is a composite track containing multiple subtracks, one for each cell type).
Most the information that you are seeking will be described in the description pages in the 2 links above. In short, from the ENCODE Txn Factor ChIP track description page:
A gray box encloses each peak cluster of transcription factor occupancy, with the darkness of the box being proportional to the maximum signal strength observed in any cell line contributing to the cluster. The HGNC gene name for the transcription factor is shown to the left of each cluster. Within a cluster, a green highlight indicates the highest scoring site of a Factorbook-identified canonical motif for the corresponding factor. (NOTE: motif highlights are shown only in browser windows of size 50,000 bp or less, and their display can be suppressed by unchecking the highlight motifs box on the track configuration page). Arrows on the highlight designate the matching strand of the motif.The cell lines where signal was detected for the factor are identified by single-letter abbreviations shown to the right of the cluster. The darkness of each letter is proportional to the signal strength observed in the cell line. Abbreviations starting with capital letters designate "ENCODE cell types":http://encodeproject.org/ENCODE/cellTypes.html identified for intensive study - Tier 1 and Tier 2 - while those starting with lowercase letters designate Tier 3 cell lines.Click on a peak cluster to see more information about the TF/cell assays contributing to the cluster, the cell line abbreviation table, and details about the highest scoring canonical motif in the cluster.
On the same track description page, you can also read more about 'score' in the methods section.
You can also find more details by searching our mailing list archives for similar previously answered questions. For example, please review this informative archived Q&A from one of the co-authors of the for the Factorbook papers. This previously answered question discusses these topics in detail, explaining that "only those clusters with a significant motif will show only one single green highlight bar, with the highest value selected."
If the above resources do not answer your questions, or if you have any follow-up questions, please feel free to reply to this forum.
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