Seqanswers Leaderboard Ad

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts
  • altodor
    Member
    • Nov 2009
    • 12

    transcription start sites (TSS)

    Hi all!

    I'm new to ChIPseq analysis and have a question regarding TSS.

    I need to compare my ChIPseq regions against transcription start sites, human. Can I download TSS from Ensembl? Is transcription start site the same as transcript start (like first nucleotide of the first exon)?

    When I tried to get them in ChIPPeakAnno package using
    EnsemblTSS<-getAnnotation(mart, featureType=c("TSS")))
    I got the same table with
    EnsemblAnnotation<-as.data.frame(getAnnotation(mart, featureType=c("TSS","miRNA", "Exon", "5utr", "3utr", "ExonPlusUtr")))
    How can it be the same?

    Thank you!
  • biznatch
    Senior Member
    • Nov 2010
    • 124

    #2
    I'm not very familiar with getting data from Ensembl, but you can get transcription start sites for all genes in the human genome from the UCSC Table Browser.

    Group: Genes and Gene Prediction Tracks
    track: UCSC Genes
    table: known genes
    output format: selected fields...

    Then click "get output" and select the fields you want, including "Transcription Start Position".

    Comment

    • kwatts59
      Member
      • Apr 2011
      • 46

      #3
      Originally posted by altodor View Post
      Is transcription start site the same as transcript start (like first nucleotide of the first exon)?
      No, the first codon of the first exon is the start codon "ATG" which also codes for methionine. This is called the translation start site.

      The transcription start site is where the RNA polymerase binds to in the 5' UTR upstream of the start codon. IMHO

      Maybe someone else can elaborate more. I dont want to give you the incorrect info.

      Comment

      • idonaldson
        Member
        • Oct 2009
        • 37

        #4
        I have done this sort of thing using the ensembl BioMart. However, the UCSC table browser for RefSeq gene annotations is my current favourite.

        Comment

        • altodor
          Member
          • Nov 2009
          • 12

          #5
          So, from Ensembl or RefSeq we get translation start sites, don't we?

          And a lot of bioconductor packages, when refering to TSS, actually give us translation start site, not transcription start site (first of all, ChiPpeakAnno)

          Does anyone use a database for TSS=transcription start sites?

          I found this discussion about TSS:

          Comment

          • Jelena
            Junior Member
            • Apr 2013
            • 2

            #6
            Originally posted by kwatts59 View Post
            No, the first codon of the first exon is the start codon "ATG" which also codes for methionine. This is called the translation start site.

            The transcription start site is where the RNA polymerase binds to in the 5' UTR upstream of the start codon. IMHO

            Maybe someone else can elaborate more. I dont want to give you the incorrect info.
            This is incorrect.

            The first codon of the first exon is approximately the transcription start site. The translation start site (i.e. the start of the CDS) is located somewhere within the transcript, but doesn't necessarily have to be in the first exon at all.

            The first nucleotide of the first exon is a good approximation. The main issue with it is that the exact TSS can shift around a bit depending on tissue and condition, so the genome annotations are only so accurate. But they're a good start.

            Comment

            Latest Articles

            Collapse

            • seqadmin
              Pathogen Surveillance with Advanced Genomic Tools
              by seqadmin




              The COVID-19 pandemic highlighted the need for proactive pathogen surveillance systems. As ongoing threats like avian influenza and newly emerging infections continue to pose risks, researchers are working to improve how quickly and accurately pathogens can be identified and tracked. In a recent SEQanswers webinar, two experts discussed how next-generation sequencing (NGS) and machine learning are shaping efforts to monitor viral variation and trace the origins of infectious...
              03-24-2025, 11:48 AM
            • seqadmin
              New Genomics Tools and Methods Shared at AGBT 2025
              by seqadmin


              This year’s Advances in Genome Biology and Technology (AGBT) General Meeting commemorated the 25th anniversary of the event at its original venue on Marco Island, Florida. While this year’s event didn’t include high-profile musical performances, the industry announcements and cutting-edge research still drew the attention of leading scientists.

              The Headliner
              The biggest announcement was Roche stepping back into the sequencing platform market. In the years since...
              03-03-2025, 01:39 PM

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, 03-20-2025, 05:03 AM
            0 responses
            49 views
            0 reactions
            Last Post seqadmin  
            Started by seqadmin, 03-19-2025, 07:27 AM
            0 responses
            57 views
            0 reactions
            Last Post seqadmin  
            Started by seqadmin, 03-18-2025, 12:50 PM
            0 responses
            50 views
            0 reactions
            Last Post seqadmin  
            Started by seqadmin, 03-03-2025, 01:15 PM
            0 responses
            201 views
            0 reactions
            Last Post seqadmin  
            Working...