Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Promoter or enhancer regions BED format

    Hi all, One can download a BED file of human genome with exonic and intronic chromosomal coordinates.

    I wanted to know if there is such a file for promoter or enhancer sites, best if it was in BED format.

    Thanks in advance. A

  • #2
    UCSC genome browser -> genome of choice (hg18 or hg19) -> Tables -> Groups(Genes...) -> Track (RefSeq)

    When you output you have the option of selecting the format (bed) and can pick whether you want the whole gene (you can then parse out the exons) or some distance up or downstream of the genes (so, say 2000bp upstream of the 5' end would be a promoter area).

    If you want enhancers you can use a track with the histone methylation/acetylation marks that correspond to enhancers (I always forget which one it is - h3k27acetylation?)

    Comment


    • #3
      enhancer associated gene

      hello,

      I have peaks which are overlapping with enhancer regions. Now, my question is which gene are regulated by these enhancers. Therefore, I need idea how can I retrieve information of genes of related enhancers. (any tool or something!!)

      Thanks.

      Comment


      • #4
        Try using the more recent Encode-derived annotation at Ensembl. ensembl.org/info/data/ftp/index.html

        Comment


        • #5
          Usually the closest genes surrounding the enhancer region are more likely to be regulated by such enhancer. This is the general assumption used in most papers I read about enhancers.

          Comment

          Latest Articles

          Collapse

          • seqadmin
            Best Practices for Single-Cell Sequencing Analysis
            by seqadmin



            While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...
            06-06-2024, 07:15 AM
          • seqadmin
            Latest Developments in Precision Medicine
            by seqadmin



            Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

            Somatic Genomics
            “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
            05-24-2024, 01:16 PM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, Yesterday, 07:24 AM
          0 responses
          9 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 06-13-2024, 08:58 AM
          0 responses
          11 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 06-12-2024, 02:20 PM
          0 responses
          16 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 06-07-2024, 06:58 AM
          0 responses
          184 views
          0 likes
          Last Post seqadmin  
          Working...
          X