Quick and Dirty Gene Network

Question

[jnf3769]

Hello all! I need to whip up a little network, preferably from known interactions, from a list of about 100 genes in Arabidopsis. All I have are the gene names. I don't care so much about up and down regulation right, just want to represent the genes interacting in one way or another--its more for demonstrative purposes than anything.

Anyone know a quick and dirty way to do this? I don't have any experience in plants so I don't know where to start here.

Answer 1

[Lars Juhl Jensen]

You could just go to the STRING database, select "Multiple proteins", paste in your gene names, and select Arabidopsis thaliana as organism. That should get you a network in no time.

[jnf3769]

This is the solution I ended up going with.

Thanks!

Answer 2

[Jean-Karim Heriche]

Try Cytoscape. Otherwise, you can extract known interactions yourself from public databases (I would use iRefIndex for this or the Arabidopsis database TAIR). In this case, you could increase coverage by transferring interactions from orthologs in other organisms. You may have to convert gene names to a suitable gene ID system.

Answer 3

[Alex Reynolds]

I worked with a couple of the post-docs in this group to post a browser for their Arabidopsis gene regulatory networks. These networks are based off of footprint calls: DNase-seq data which show TF binding in gene promoters make the TF gene a "regulator" of the promoter's gene.

Answer 4

[vakul.mohanty]

Netwalker (https://netwalkersuite.org/) can take your gene names and build interaction networks for you based on multiple curated interaction data sets. It will give you a network and you can play with the outlay, group genes, analyze pathway enrichment. Just load your files select the gene names column in click on rownames and then on Plot Network. Hope that helps.