Question: How to get short and sweet gene names/description for gene IDs?
1
gravatar for Wox
13 months ago by
Wox320
HUJI
Wox320 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 • 399 views
ADD COMMENTlink modified 13 months ago by finswimmer13k • written 13 months ago by Wox320
5
gravatar for finswimmer
13 months ago by
finswimmer13k
Germany
finswimmer13k 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 13 months ago by finswimmer13k

Thank a heaps finswimmer :)

ADD REPLYlink written 13 months ago by Wox320
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