Question: Regulatory Network Tool
0
gravatar for rvrob3000
14 months ago by
rvrob30000
rvrob30000 wrote:

Hi everyone,

I have been looking for a tool in order to build a gene regulatory network. Long story short, I have a set of Arabidopsis gene identifiers and I would want to upload these gene identifiers into a program that would be able to create a gene regulatory network for me. Unfortunately, all the programs I have found require some sort of expression data, which I do not have. So does anyone know of a gene regulatory network tool that can create regulatory networks from gene identifiers or at least uniprot accession numbers only without needing to have expression data?

Thank You,

ADD COMMENTlink modified 14 months ago by genomax51k • written 14 months ago by rvrob30000
1

If it was as easy as getting a list of gene IDs and nothing else .... we would have solved the worlds health problems 100 years ago.

Do you have anything at all that links those genes? have you randomly selected them? where did the list come from?

ADD REPLYlink modified 14 months ago • written 14 months ago by YaGalbi1.3k

Hi Kenneth,

No I don't have anything that links the genes. The list would come from a large proteomics data set. I know they are transcription factors from the GO annotations and TAIR descriptions.

ADD REPLYlink written 14 months ago by rvrob30000

A "large proteomics dataset" could mean a lot of things. Input the gene identifiers into StringDB and you will see the kind of network you get. My guess is that if the gene list is not filtered to included only those IDs with some biological connection that you are testing (e.g. co-expression or tissue specificity) then your result will just be a load of nodes with very few edges.

An alternative is i-regulon which may give similar results.

However, you may get lucky! So give them a try.

ADD REPLYlink modified 14 months ago • written 14 months ago by YaGalbi1.3k

Searching in ppi database is a good place to start with, since the questioner doesn't have any information about how two genes should be connected. This will work if the questioner's gene regulatory network is equal to ppi network.

ADD REPLYlink modified 14 months ago • written 14 months ago by solo777350

Maybe you could try to map some of your genes to pathways like in KEGG and then you will be able to plot a regulatory network.

ADD REPLYlink written 14 months ago by solo777350

That would be good.... but how would you select "some" of the genes? IF random....you'd have to be pretty lucky to find anything. "Some" of the genes are usually selected by co-expression .... the filtering/selection process is the key to getting the network. The tool that builds the network is just a tool..and it follows the same rules as all other tools...."Rubbish In, Rubbish Out".

ADD REPLYlink written 14 months ago by YaGalbi1.3k

Hi solo7773,

I tried that. A lot of them don't have KO's assigned to them. For example if I were to search for "AT1G30330", it doesn't have a K number and there are no pathways assigned to it.

http://www.genome.jp/dbget-bin/www_bget?ath:AT1G30330

ADD REPLYlink written 14 months ago by rvrob30000

That indeed happens as the database only stores the knowledge we've learned. Another choice, maybe you can try to search a bioinformatic tool that can generate/predict a regulatory network (or regulatory interactions) based on gene list. After that, you will be able to use any tools like cytoscape to make a network visualisation.

ADD REPLYlink modified 14 months ago • written 14 months ago by solo777350
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1539 users visited in the last hour