Question: Quick and Dirty Gene Network
1
gravatar for jnf3769
3.8 years ago by
jnf376940
United States
jnf376940 wrote:

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.

ADD COMMENTlink modified 3.8 years ago by vakul.mohanty240 • written 3.8 years ago by jnf376940
5
gravatar for Lars Juhl Jensen
3.8 years ago by
Copenhagen, Denmark
Lars Juhl Jensen11k wrote:

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.

ADD COMMENTlink written 3.8 years ago by Lars Juhl Jensen11k

This is the solution I ended up going with.

Thanks!

ADD REPLYlink written 2.4 years ago by jnf376940
0
gravatar for Jean-Karim Heriche
3.8 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche24k wrote:

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.

ADD COMMENTlink written 3.8 years ago by Jean-Karim Heriche24k
0
gravatar for Alex Reynolds
3.8 years ago by
Alex Reynolds31k
Seattle, WA USA
Alex Reynolds31k wrote:

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.

ADD COMMENTlink written 3.8 years ago by Alex Reynolds31k
0
gravatar for vakul.mohanty
3.8 years ago by
vakul.mohanty240
United States
vakul.mohanty240 wrote:

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.

ADD COMMENTlink written 3.8 years ago by vakul.mohanty240
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