Hi Guo,
The difference between Peaks and Raw Signal is described in the HAIB
TFBS track
(http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeHudsonalphaChipSeq);
here is an excerpt:
/Peaks/
Sites with the greatest evidence of transcription factor binding.
/Raw Signal/
A continuous signal which indicates density of aligned reads. The
sequence reads were extended to the size-selected length (225 bp),
and the read density computed using the bedItemOverlapCount utility.
This annotation was generated by the ENCODE Data Coordination Center
at UCSC.
Please see this session in which I have opened a sample region of the
Txn Factor ChIP data and the BATF subtracks from HAIB TFBS:
http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Katrina&hgS_otherUserSessionName=BATF%20for%20mlq.
Look for the items in Txn Factor ChIP track that say "BATF" on the
left-hand side of the item. You can see these do correspond with the
items from HAIB TFBS that I have open, which are the experiments for
BATF. The BATF items in the Txn Factor ChIP track were incorporated into
this track from the HAIB TFBS peak data.
Please don't hesitate to contact the mail list again if you have any
further questions.
Katrina Learned
UCSC Genome Bioinformatics Group
Guo An-Yuan wrote, On 12/09/10 16:59:
> Thanks. So what is the different of "Peaks" and "Raw Signal"? I think if I
> just need the potential TFBS, can I just use "Peaks" and don't use "Raw
> Signal".
> I have compared the HAIB "Peaks" for TF "BATF" and Txn Factor ChIP data.
> But I didn't find the same peak location for BATF. As you said in this
> email, the HAIB "Peaks" should be included in the Txn Factor ChIP data.
> Are they from same raw data and different peak find method, so the peaks
> are different? Which should I use?
> thanks very much
>
> Anyuan
>
> 于 2010-12-10 3:33, Vanessa Kirkup Swing 写道:
>
>> Dear Anyuan,
>>
>> The data in the ENCODE Regulation Txn Factor ChIP Track is only a subset of
>> the data included HAIB TFBS and Yale TFBS tracks. The HAIB TFBS and Yale
>> TFBS tracks contain additional views such as "Raw Signal" and "Signal"
>> whereas the Txn Factor ChIP Track utilizes data from only the "Peaks" view
>> from the those tracks.
>>
>> If you have further questions, please contact the mailing list.
>>
>> Vanessa Kirkup Swing
>> UCSC Genome Bioinformatics Group
>>
>>
>> Subject:
>> inquire about UCSC Chip-seq data
>> From:
>> 郭安源<[email protected]>
>> Date:
>> Thu, 09 Dec 2010 10:49:09 +0800
>> To:
>> [email protected]
>>
>> Dear sir,
>> Thanks for your great work about UCSC genome browser.
>> I have a question about the human Chip-Seq data.
>> At human hg18, under "Regulation" super tracks,there are tracks named "ENCODE
>> Integrated Regulation Tracks-Txn Factor ChIP", "HAIB TFBS", "Yale TFBS". I
>> want
>> to know that whether the data in "ENCODE Integrated Regulation Tracks-Txn
>> Factor
>> ChIP" contains all the data in tracks "HAIB TFBS" and "Yale TFBS". Since I
>> saw
>> the following words on the track pages
>> http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=174800793&c=chr1&g=wgEncodeRegTfbsClustered
>> http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=174800793&c=chr1&g=wgEncodeHudsonalphaChipSeq
>> http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=174800793&c=chr1&g=wgEncodeYaleChIPseq
>> So if want a complete chip-seq data, need I download all these or just the
>> Txn
>> Factor ChIP track?
>>
>> Thanks very much.
>>
>> Anyuan Guo
>>
>> Description
>>
>> This track shows regions where transcription factors, proteins responsible
>> for
>> modulating gene transcription, bind to DNA as assayed by ChIP-seq (chromatin
>> immunoprecipitation with antibodies specific to the transcription factor
>> followed by sequencing of the precipitated DNA). Additional views of this
>> data
>> set and additional documentation on the methods used for this track are
>> available at the Yale TFBS Track
>> <http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=wgEncodeYaleChIPseq> and the
>> HAIB
>> TFBS Track
>> <http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=wgEncodeHudsonalphaChipSeq>
>> pages.
>> The /Peaks / views in those pages are the basis for the clusters shown here,
>> which combine data from the peaks from the different cell lines and different
>> transcription factors in those pages.
>>
>> Credits
>>
>> This track shows data from the Myers Lab<http://myers.hudsonalpha.org/> at
>> the
>> HudsonAlpha Institute for Biotechnology<http://www.hudsonalpha.org/> and by
>> the
>> labs of Michael Snyder<http://snyderlab.stanford.edu/>, Mark Gerstein
>> <http://bioinfo.mbb.yale.edu/> and Sherman Weissman
>> <http://info.med.yale.edu/bcmm/SMW/SMWhome2.html> at Yale University; Peggy
>> Farnham<http://www.genomecenter.ucdavis.edu/farnham/> at UC Davis; and Kevin
>> Struhl<http://struhl.med.harvard.edu/> at Harvard.
>>
>> On the HAIB TFBS page, it shows "These data were provided by the Myers Lab
>> <http://myers.hudsonalpha.org/> at the HudsonAlpha Institute for
>> Biotechnology
>> <http://www.hudsonalpha.org/>.".
>> On the Yale TFBS track page, it shows "These data were generated and
>> analyzed by
>> the labs of Michael Snyder<http://www.yale.edu/snyder/>, Mark Gerstein
>> <http://bioinfo.mbb.yale.edu/> and Sherman Weissman
>> <http://info.med.yale.edu/bcmm/SMW/SMWhome2.html> at Yale University; Peggy
>> Farnham<http://www.genomecenter.ucdavis.edu/farnham/> at UC Davis; and Kevin
>> Struhl<http://struhl.med.harvard.edu/> at Harvard. Contact: the Gerstein lab
>> <mailto:[email protected]>. ".
>>
>>
>
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