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  • enrichment profile

    Hi,
    Could somebody please explain me in more details (containing which commands, scripts, ... ) how they provided chip-seq enrichment profile over gene bodies in the attached figure?

    they explained in their article:

    "Composite profile of genes with gene bodies marked by H3K36me3 and DNA
    methylation over at least 20% of gene body length. Each gene body was divided into 20 bins. Sequences up to 5 kb upstream of the TSS and 5 kb
    downstream of the 3’ gene end were divided into 10 bins"

    Profiles at the gene body and promoter
    The hg18 RefSeq database (http://hgdownload.cse.ucsc.edu/ goldenPath/hg18/database/) was used for annotation. The promoter region was defined as +/-500 bp relative to the transcription start site, and ‘gene body’ was defined as from the transcription start site to the end of the transcript. For DNA methylation and histone modifications, the average log2 ratios of probes falling into promoters or gene bodies were calculated. For CpG count in the gene body, the number of CpG dinucleotides within gene bodies was counted and divided by the length of the gene body and then scaled to counts per 1 kb.


    Thank you so much
    Attached Files

  • #2
    Plotting Methyylation density vs TSS

    I have related question. Though it is not a sequencing question. However I would like to undertsand that, how I can generate a plot similar to Fig 2 A of this paper http://www.biomedcentral.com/1471-2164/11/137
    I have beta values from array experiment and want to plot - TSS on X axis and methylation on Y-axis.

    Any suggestion.

    Thanks.

    Comment


    • #3
      Originally posted by maria_mari View Post
      Hi,
      Could somebody please explain me in more details (containing which commands, scripts, ... ) how they provided chip-seq enrichment profile over gene bodies in the attached figure?

      hi

      simon anders wrote a nice tutorial on how to do visualization on seq data including the type of plots you refer to: http://www.bioconductor.org/packages...HilbertVis.pdf

      it is not exactly what you want as it does not include binning of genes but you should get the concept and do the rest yourself.

      and, of course, you could ask the authors of the paper for their scripts. did you do that?

      Comment


      • #4
        In case you prefer Python to R, I've recently written a similar explanation on how to do this with Python and our HTSeq framework: http://www-huber.embl.de/users/anders/HTSeq/

        Make sure to read the section "Tour through HTSeq" before the section "A detailed use case: TSS plots", otherwise it might be hard to understand.

        Comment


        • #5
          enrichment plot for methylation data

          Thanks Simon,
          let me clarify, I have methylation array based data where I have one probe with corresponding coordinate, and beta values. I want plot these beta values in a set of bins agains human TSS sites. Will the array based data work in same way as that of seq data
          Thanks

          Comment


          • #6
            seqminer

            maria_mari ,

            Seqminer may serve your purpose too.

            Comment


            • #7
              Hi Maria_mari,

              We have a very similar plot in our NAR paper that averages over genes http://nar.oxfordjournals.org/content/39/17/7415.long
              The R code is also available as Supp information and these and other visualizations can be found in the Repitools package in bioconductor.

              Comment


              • #8
                P.S. What is the article that you are referring to?

                Comment


                • #9
                  To elucidate the relationship between intragenic DNA methylation and chromatin marks, we performed epigenetic profiling of chromosome 19 in human bronchial epithelial cells (HBEC) and in the colorectal cancer cell line HCT116 as well as its counterpart with double knockout of DNMT1 and DNMT3B (HCT116-DKO). Analysis of H3K36me3 profiles indicated that this intragenic mark of active genes is associated with two categories of genes: (i) genes with low CpG density and H3K9me3 in the gene body or (ii) genes with high CpG density and DNA methylation in the gene body. We observed that a combination of low CpG density in gene bodies together with H3K9me3 and H3K36me3 occupancy is a specific epigenetic feature of zinc finger (ZNF) genes, which comprise 90% of all genes carrying both histone marks on chromosome 19. For genes with high intragenic CpG density, transcription and H3K36me3 occupancy were not changed in conditions of partial or intensive loss of DNA methylation in gene bodies. siRNA knockdown of SETD2, the major histone methyltransferase responsible for production of H3K36me3, did not reduce DNA methylation in gene bodies. Our study suggests that the H3K36me3 and DNA methylation marks in gene bodies are established largely independently of each other and points to similar functional roles of intragenic DNA methylation and intragenic H3K9me3 for CpG-rich and CpG-poor genes, respectively.

                  Comment


                  • #10
                    BS-seq plot

                    Hi,everyone!
                    I'm handling with some BS-seq(bisulfite-sequencing)data,but i have same question described above(like TSS plots described as maria_mari asked).I have the data including pecent methylation in a particular chromosome site of Arabidopsis and the annotation file(gff),How can i plot it? Is there any python or R script available for me?
                    Thank you!
                    Last edited by wuzefeng2012; 09-24-2013, 07:24 PM.

                    Comment

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