Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Circos for GSEA

    Hi,

    I quite like the look of Circos plots and was wondering if the following is possible before I embark on what appears to be a steep learning curve to get the job done.

    I have GSEA results from two distinct experiments (same organism, different models).
    In place of performing a simple intersection of the results (and displaying a list of gene sets enriched in both datasets) I would like to present a circos plot that displays the underlying similarity in the gene sets at the gene level.

    I envisage the plot would be something like this:
    -2 hemispheres which represent each experiment.
    -The outer track contains the gene set names (color coded for enrichment score or possibly arbitrarily colored but matched between hemispheres)
    -The inner track contains the genes within the gene set (color coded for fold-change)
    -Connections are made between the hemispheres only if the gene is dysregulated in the same direction

    Is such at task possible. Is circos the right tool for the job. As mentioned above the idea is to go beyond GSEA and provide visual information about the similarity of a given gene set between the two models.

    Cheers,
    Aaron

  • #2
    There have been quite a few views but no replies as of yet.

    Is there any further information or clarification required to get some feedback on this?

    Cheers,
    Aaron

    Comment


    • #3
      Hi Aaron,

      I think circos is definitely the right tool for the job because of its flexibility - you can basically plot whatever you want. What you have mentioned would require a heatmap track and a link track. Both of these are easily achieved with Circos.

      The tricky part would be getting your data into the right format. I'd say a few python scripts to turn your data into a nice table would do the job!

      Best,

      Matt.

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Strategies for Sequencing Challenging Samples
        by seqadmin


        Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
        03-22-2024, 06:39 AM
      • seqadmin
        Techniques and Challenges in Conservation Genomics
        by seqadmin



        The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

        Avian Conservation
        Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
        03-08-2024, 10:41 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Yesterday, 06:37 PM
      0 responses
      10 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:07 PM
      0 responses
      9 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      50 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-21-2024, 07:32 AM
      0 responses
      67 views
      0 likes
      Last Post seqadmin  
      Working...
      X