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

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
network cytoscape
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updated by Ram Ram • written by SheelS • SheelS

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."

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updated by Ram Ram • written by Neilfws Neilfws

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,

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updated by Ram Ram • written by SheelS • SheelS

1 answer

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,

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updated by Ram Ram • written by mary99 • mary99

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

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written by Sib • Sib

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