About transcription factor ChIP-seq

[Yuchen Feng]

Hello sir or madam:

I am a PhD student of the university of Newcastle. I got some very useful information from transcription factor ChIP-seq from ENCODE. One thing I don't understand  is that if you click into one TF such as MYC, it will show Assays for MYC in Cluster and Assays for MYC Hits in cluster. I don't know what does Hits mean?

Thank you for your help. 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 

[Brian Lee]

Dear Yuchen,

Thank you for using the UCSC Genome Browser and your question about interpreting the the ChIP-Seq Transcription Factor Binding Site (TFBS) track.

The track is a summary of many other experiments that were done during the second stage of the ENCODE project (the data has not been updated at UCSC since 2012). This clusters track takes many thousands of experiments and attempts to summarize them in a single track on the human genome. When you click into the track, the list of underlying experiments that support the annotation in that location are listed. This allows researchers that are interested in exploring further to both visualize those underlying tracks, or to acquire the data from them to analyze them further.

Here is a session link (you can make sessions of your own under the "My Data" menu) that visualizes this around a specific region: http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doLoadUrl=submit&hgS_loadUrlName=http://genome.ucsc.edu/goldenPath/help/examples/sessions/session.hg19.TFBScluster

This session helps illustrate the process behind creating the TFBS Clusters track. Uniform processing of ENCODE experiments resulted in a comparable signal scores viewable in a further track defined as wgEncodeAwgTfbsUniform, that was then used to generate the clustered score that goes into the condensed defined wgEncodeRegTfbsClusteredV3 track, where a normalization factor was used to attempt to better distribute scores evenly. The session originated from a mailing list question regarding whether it was correct to interpret the darker score as increased biological evidence of binding for a transcription factor at a particular spot. The response shared how by filtering to display only the JUN, JUNB, JUND, and MYC factors you can see several individual "Uniform ...c-Myc" tracks displayed below the clusters track. Those are the separate wgEncodeAwgTfbsUniform tracks used to generate the processed clustered summary wgEncodeRegTfbsClusteredV3 track for this MYC cluster. Those individual uniform processed scores were used to create the cluster score given to the MYC cluster. Like the MYC factor, you can also click the JUN factors and you will see there is only one observed cell type where this data indicates this factor binds at this location. And similarly below, you will see the "Uniform... Jun" tracks that contributed to the clusters track.

Often reading the track description pages for these tracks is the best way to learn more (and see publications to read even further materials). Here are some links to the above mentioned tracks.

The TFBS Clusters track:

http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegTfbsClusteredV3

The Uniform TFBS track that provided the input for the TFBS clusters track:

http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeAwgTfbsUniform

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further public questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee

UC Santa Cruz Genomics Institute

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