How to prepare a input data for Cytoscape, genetic network software

Question

[SheelS]

Hi all,

I am using a software called Cytoscape to construct my interested genetic network, unfortunately this is my first time to do this, therefore I met some simple questions.

My question is, I only have a list of candidate genes' name, for example (as below), as I know, at least two columns are necessary for as the input data for Cytoscape software, therefore, how or where could I get more information (or materials) to run this software.

Below is the gene list I feel interested, (I have used Genemania and I wanna try different software products to see can I get different results and compare them) Many thanks for help, appreciates.

INHBB
MAGI2
MAP3K9
NCAPD2
PRUNE
RARS

[Neilfws]

You need at least 2 columns because a network is a set of pairwise interactions. There is no indication from your gene list of what those interactions are. I think you need to figure out the research question and the required data before simply "trying different software."

[SheelS]

Hi there,

Appreciates for your reply, the aboved gene list is just a part of my interested list (as an example to present my question), but just wonder that how or where could I find the interaction between the genes? Could you please kindly explain more about this? For example, the database I can use, then I may be able to find the interaction between my candidate genes or information and so on.

Thanks,

Answer 1

[mary99]

Hello all,

I have the same question.If I have just the list of genes how can I find the interaction between the genes?

Thanks,

[roy.granit]

If the list is short you might just use some online tools like:

• http://string-db.org/
• http://www.genemania.org/

If you have a long list of genes, I would recommend inserting them into Cytoscape and using the following plugin to uncover the known interactions between genes

http://wiki.reactome.org/index.php/Reactome_FI_Cytoscape_Plugin_3

[Sib]

I have the same question as above. How can I use STRING DB to prepare input for Cytoscape?