How to prepare a input data for Cytoscape, genetic network software
1
1
Entering edit mode
10.5 years ago
SheelS ▴ 40

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 • 9.7k views
ADD COMMENT
3
Entering edit mode

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."

ADD REPLY
0
Entering edit mode

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,

ADD REPLY
0
Entering edit mode
9.4 years ago
mary99 ▴ 80

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,

ADD COMMENT
1
Entering edit mode

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

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1504 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6