question about ENCODE experiment IDs and scores

[Eric Foss]

Dear UCSC Genome Browser, 

I am looking for transcription factor binding sites. I downloaded two files of data from ENCODE using the Table Browser: "Txn Fac ChIP” and “Txn Fac ChIP V2”. The settings I used for one of these downloads are shown on the attached screen shot. The Table Schema describes the last two columns as experiment IDs and experiment scores, but I can’t find a description of what these two things mean. Could you please let me know specifically what these mean? 

Thank you. 

Eric

Seattle

[Brian Lee]

Dear Eric,

Thank you for using the UCSC Genome Browser and your question about the last two columns in the Txn Fac ChIP tables referring to experiment IDs and experiment scores.

When viewing the Table Schemas in the Table Browser, if you scroll down you should see a Track Description page, such as the below:

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

http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegTfbsClusteredV2

Reviewing these Track Descriptions will often help provide more details than the one line in the schema details including these sentences: "The first list field (expNums) contains numeric identifiers for experiments, keyed to the wgEncodeRegTfbsClusteredInputsV3 table, which includes such information as the experiment's underlying Uniform TFBS table name, factor targeted, antibody used, cell type, treatment (if any), and laboratory source. The second list field (expScores) contains the scores for the corresponding experiments."

Also on theTrack Description page you will find a "downloads" link that will bring you to a page where you can quickly acquire files, versus using the Table Browser to output the information to a named.txt file. In this case you could click the links for the wgEncodeRegTfbsClusteredV2.bed.gz and wgEncodeRegTfbsClusteredV3.bed.gz files: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeRegTfbsClustered/

In essence these final two columns are metaData sharing coded information through further associated tables to explain the experimental cell types providing evidence for transcription factor binding at each location. If this information is not of interest, you could ignore those last two columns. Please see this previously answered mailing list question for further information:

https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/93Rqrrs--y8/VceGRwgyh88J

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further 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

UCSC Genome Bioinformatics Group

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