pathway or network from DEG list tool (plant)

Question

[manekineko]

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?

Answer 1

[Leite]

Hey dear

You can try GeneMANIA using Arabidopsis thaliana as model. >

You can also try STRING

Best, Leite

[manekineko]

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

[Leite]

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

[manekineko]

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

[Leite]

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.