User:Karmella Haynes/Notebook/PcTF Genomics/2014/07/23

From OpenWetWare
Jump to: navigation, search
Owwnotebook icon.pngPc-TF Genomics Report.pngMain project page
Resultset previous.pngPrevious entry      Next entryResultset next.png


  • 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:
    • 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)