Question: How to get short and sweet gene names/description for gene IDs?
1
gravatar for Wuschel
5 weeks ago by
Wuschel120
HUJI
Wuschel120 wrote:

I am working on Arabidopsis thaliana omics project. How can I get short and proper gene description for each AGI (Gene IDs) numbers? Downloaded database from Tair10 has pretty lengthy names which are difficult to work with (plotting , summarizing in downs-stream works)

e.g.

AT1G01050       Soluble inorganic pyrophosphatase 1 OS=Arabidopsis thaliana (sp|q93v56|ipyr1_arath : 419.0)

AT1G01800   Enzyme classification.EC_1 oxidoreductases.EC_1.1 oxidoreductase acting on CH-OH group of donor(50.1.1 : 434.7) & (+)-neomenthol dehydrogenase OS=Arabidopsis thaliana (sp|q9m2e2|sdr1_arath : 357.0) (original description: none)

From where I can get / how to modify the names short and sweet?

rna-seq R proteomics • 153 views
ADD COMMENTlink modified 5 weeks ago by finswimmer11k • written 5 weeks ago by Wuschel120
5
gravatar for finswimmer
5 weeks ago by
finswimmer11k
Germany
finswimmer11k wrote:
  • Go to ensembl's BioMart
  • Choose Dataset: Ensembl Plant Genes and Arabidopsis thaliana genes
  • Choose Filters->Genes -> Input external references ID list -> Gene Stable ID(s) and paste your IDs into the textfield
  • Choose Attributes->Gene and select Gene Stable ID and Gene name
  • Click Result and download in the format you like

You can extract the IDs from the file example above with a simple cut -f1 input_file > gene_ids.txt.

fin swimmer

ADD COMMENTlink written 5 weeks ago by finswimmer11k

Thank a heaps finswimmer :)

ADD REPLYlink written 4 weeks ago by Wuschel120
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1176 users visited in the last hour