User:Karmella Haynes/Notebook/PcTF Genomics/2014/07/23: Difference between revisions

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|style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]]<span style="font-size:22px;">Pc-TF Genomics</span>
|style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]]<span style="font-size:22px;">Pc-TF Genomics</span>
|style="background-color: #F2F2F2" align="center"|<html><img src="/images/9/94/Report.png" border="0" /></html> [[{{#sub:{{FULLPAGENAME}}|0|-11}}|Main project page]]<br />{{#if:{{#lnpreventry:{{FULLPAGENAME}}}}|<html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>[[{{#lnpreventry:{{FULLPAGENAME}}}}{{!}}Previous entry]]<html>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</html>}}{{#if:{{#lnnextentry:{{FULLPAGENAME}}}}|[[{{#lnnextentry:{{FULLPAGENAME}}}}{{!}}Next entry]]<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html>}}
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'''Promoters research'''<br>
'''Promoters research'''<br>
* Found free promoters database at the Eukaryotic Promoter Database website
* Found free promoters database at the Swiss Institute of Bioinformatics Eukaryotic Promoter Database (EPD) website
* Retrieved BED file of all human promoters from: http://epd.vital-it.ch/get_promoters.php
* Retrieved BED file of all human promoters from: http://epd.vital-it.ch/get_promoters.php
** Selected H. sapiens, left all other options blank, clicked [select], downloaded BED file, uploaded to Galaxy as Promoters EPD All
** Selected H. sapiens, left all other options blank, clicked [select], downloaded BED file, uploaded to Galaxy as Promoters EPD All

Latest revision as of 00:07, 27 September 2017

Pc-TF Genomics Main project page
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07/23/14

  • ChIPseq - bioinformatics

Promoters research

  • Found free promoters database at the Swiss Institute of Bioinformatics Eukaryotic Promoter Database (EPD) website
  • Retrieved BED file of all human promoters from: http://epd.vital-it.ch/get_promoters.php
    • Selected H. sapiens, left all other options blank, clicked [select], downloaded BED file, uploaded to Galaxy as Promoters EPD All
    • Total promoters: 23,316
    • Each is only 10 bp long
    • Gene names are included!
  • Note: Custom-generated promoter file (500 bp TSS regions) = 26,960. This is over 3k more than the EPD.

New Galaxy files
Note: EPD allows selection of promoter sub-classes

    • All EPD promoters - uploaded as Promoters EPD All
    • TATA-box motif - Promoters EPD TATA = 2,007 regions
    • Initiator motif - Promoters EPD Init = 6,538 regions
    • CCAAT-box motif - Promoters EPD CCAAT = 3,838 regions
    • GC-box motif - Promoters EPD GC = 10,695 regions
    • CpG (unable to retrieve...looks like criteria have not been added yet)



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