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

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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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|style="background-color: #F2F2F2" align="center"|[[File:Report.png|frameless|link={{#sub:{{FULLPAGENAME}}|0|-11}}]][[{{#sub:{{FULLPAGENAME}}|0|-11}}|Main project page]]<br />{{#if:{{#lnpreventry:{{FULLPAGENAME}}}}|[[File:Resultset_previous.png|frameless|link={{#lnpreventry:{{FULLPAGENAME}}}}]][[{{#lnpreventry:{{FULLPAGENAME}}}}{{!}}Previous entry]]&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;}}{{#if:{{#lnnextentry:{{FULLPAGENAME}}}}|[[{{#lnnextentry:{{FULLPAGENAME}}}}{{!}}Next entry]][[File:Resultset_next.png|frameless|link={{#lnnextentry:{{FULLPAGENAME}}}}]]}}
 
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==mm/dd/yy==
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==07/23/14==
 
<!-- Precede finished items with a checkmark &#x2713; -->
 
<!-- Precede finished items with a checkmark &#x2713; -->
* PcTF ChIPseq
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* ChIPseq - bioinformatics
  
 
----
 
----
 
'''Promoters research'''<br>
 
'''Promoters research'''<br>
* Found free promoters database at the Eukaryotic Promoter Database website
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* 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
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** 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)
  
  

Latest revision as of 00:07, 27 September 2017

Owwnotebook icon.pngPc-TF Genomics Report.pngMain project page
Resultset previous.pngPrevious entry      Next entryResultset next.png


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)