Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • bioBob
    replied
    Hi,

    thanks for the reply. That is the target id. From miRDB:

    mmu-miR-669f-3p NM_001042565 99.7800236967459

    I suppose I could get around the ensembl id's by using gene name, but I still need a way to bulk convert the id's to gene names.

    Leave a comment:


  • yueluo
    replied
    Took a quick look at both Ensembl and Ncbi considering the transcript "NM_001042565". I tried its gene "Wsb1" to get all the transcript information.

    NM_001042565.3 = ENSMUST00000017821 (Wsb1-001)
    NM_019653.3 however, has no corresponding Ensembl transcript.

    This would probably be why NM_001042565 doesn't get converted, since biomart would not contain an id-id mapping information for such transcript.

    Anyway, what does the original "miRDB target id" look like?

    Leave a comment:


  • bioBob
    started a topic converting mirDB target ids to ensembl ids

    converting mirDB target ids to ensembl ids

    Hi,

    I have about 3000 miRNA targets from miRDB. I am needing to convert the target identifiers into Ensembl ids (mouse btw). About 2k of these convert using biomaRt in R. The other 1k I am not sure how to handle programmatically as I can't figure out what id type they are.

    Most convert using either refseq_mrna (Refseq mRNA ID(s) [e.g. NM_001195244]) or refseq_mrna_predicted (Refseq Predicted mRNA ID(s) [e.g. XM_889253])

    An example of one that doesn't convert: "NM_001042565". Looking this up in Ensembl via the main search I get "novel transcript (Mouse Transcript)". So I know it is there. I have taken the identifier and tried to convert it using Ensembl's BioMart using the filter option with most of the gene/transcript looking options and do not get anything back.

    What filter option should I use to get all the miRDB target id's to convert to Ensembl IDs???

    Thanks,
    Bob

Latest Articles

Collapse

  • seqadmin
    Essential Discoveries and Tools in Epitranscriptomics
    by seqadmin




    The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
    04-22-2024, 07:01 AM
  • seqadmin
    Current Approaches to Protein Sequencing
    by seqadmin


    Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
    04-04-2024, 04:25 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 04-11-2024, 12:08 PM
0 responses
59 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 10:19 PM
0 responses
57 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 09:21 AM
0 responses
53 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-04-2024, 09:00 AM
0 responses
56 views
0 likes
Last Post seqadmin  
Working...
X