Question: Getting the function of genes based on gene names
1
gravatar for GabrielMontenegro
3.5 years ago by
United Kingdom
GabrielMontenegro530 wrote:

I have a list of gene names and I want to know the function of each gene. I tried using the Biomart website but couldn't find a list with gene function. For instance, is it possible to get the CC, MF, and BP GO terms from that website?

genome • 3.3k views
ADD COMMENTlink modified 3.5 years ago by Giovanni M Dall'Olio26k • written 3.5 years ago by GabrielMontenegro530

A: Clustering Genes in a Genome based on GO Terms

A: focus on specific pathway

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by EagleEye6.4k
1
gravatar for Antoine
3.5 years ago by
Antoine10
FR/PARIS/CNRS-INSERM-CNAM-P7
Antoine10 wrote:

From Biomart, you can easily obtain the GO CC, MF and BP you are looking for:

  1. Choose Ensembl database 83 for example
  2. Choose your organism (S. cerevisiae for example)
  3. OPTIONAL : If you want info on a subset of genes only : click on FILTER and add your gene list in the Input external references ID list textbox
  4. Click on ATTRIBUTES then EXTERNAL
  5. Tick the box for the go term
  6. Click on result at the top of the page to visualize or download them!

Example : http://www.ensembl.org/biomart/martview/73fed257731b73cebf31e71a3e933b2d

edit : Optional point added as suggested by Emily_Ensembl

ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by Antoine10

If you're not familiar with BioMart, you could take a look at the video tutorial.

ADD REPLYlink written 3.5 years ago by Emily_Ensembl19k

You should also probably add in step 2B: filter by your list of gene names.

ADD REPLYlink written 3.5 years ago by Emily_Ensembl19k
0
gravatar for genomax
3.5 years ago by
genomax71k
United States
genomax71k wrote:

Here are two site1 site2.

ADD COMMENTlink written 3.5 years ago by genomax71k
0
gravatar for Giovanni M Dall'Olio
3.5 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

You can try Enrichr, an online gene enrichment tool which features many databases.

Just copy&paste the list of gene symbols, and then select the enrichment dataset you prefer. In your case I would look at the pathways and ontologies.

ADD COMMENTlink written 3.5 years ago by Giovanni M Dall'Olio26k
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