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

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==mm/dd/yy==
==07/23/14==
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* PcTF ChIPseq
* ChIPseq - bioinformatics


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* Found free promoters database at the Eukaryotic Promoter Database website
* Found free promoters database at the Eukaryotic Promoter Database 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
** Selected H. sapiens, left all other options blank, clicked [select], downloaded BED file, uploaded to Galaxy as Promoters EPD All
** Total promoters: 23,316
** Total promoters: 23,316
** Each is only 10 bp long
** Gene names are included!
** 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'''<br>
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)




Revision as of 15:28, 23 July 2014

Pc-TF Genomics <html><img src="/images/9/94/Report.png" border="0" /></html> Main project page
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07/23/14

  • ChIPseq - bioinformatics

Promoters research

  • Found free promoters database at the Eukaryotic Promoter Database 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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