This is a test version of Biostars. For the public version, visit https://www.biostars.org.
pathway or network from DEG list tool (plant)

I have a list of DEG genes (e.g. T459_18598, from a plant in Ensembl), what tool I can use to see if there is a genes connected to each other forming a pathway or a network or connected by a function. The problem is that the plant (pepper) is not so popular among such tools and well-annotated?

deg network pathway
• 1,958 views • link
updated by Leite Leite • written by manekineko manekineko

1 answer

Hey dear

You can try GeneMANIA using Arabidopsis thaliana as model. >

You can also try STRING

Best, Leite

• 0 views • link
written by Leite Leite

Unfortunately, STRINGS do not have pepper as an organism afaik.

• 0 views • link
written by manekineko manekineko

Dear @manekineko

Often the organism we work with is not available or has little information, but we can use another as a knowledge base.

Once worked with goat and since I didn't have much information I used Bos taurus to build my network

• 0 views • link
written by Leite Leite

I agree, but I cannot find a way to intersect my accession numbers to let say with tomato or closer organism.....

• 0 views • link
written by manekineko manekineko

First, you need to find out which is the closest organism that has interaction data available. Then you have to change the access to a more general nomenclature, maybe the name gene.

• 0 views • link
written by Leite Leite

Log in to answer this question.

More posts like this