Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • GO analysis - with or without isoforms

    Hiya,

    I have a blast database for GO terms in blast2go which includes IDs for all the isoforms of the genes. When I make my gene lists for GO enrichment analysis, ithe list compiler pulls the IDs of all the isoforms associated with the genes of interest (DEG). My question is : Should I

    (a) De-duplicate the list so just one ID per gene is input into the GO enrichment analysis

    or

    (b) Submit the full list containing the IDs of all the isoforms for each gene of interest?

    I have run both and the de-duplicated list as I anticipated contains less GO terms than the full list containing all the isoforms.

    I feel like it is correct to run the full list of IDs (option b) because otherwise the enrichment test could be negatively biased by terms where there are lots of isoforms present in the database, but only one is submitted - making it look like the GO term is less enriched than it actually is (I hope that makes sense).

    Best wishes and any opinions/advice are greatly appreciated

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
49 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