Tool to create gene edge

Question

[saj98]

Hello everyone

I am doing RNA seq network analyses by using cytoscape. I have problem to create gene edge; does any one have experience with gene edge preparation?

Best
Shaima

[Sean R Johnson]

I think this question is unclear. Is it that you want your gene names to be the nodes, and you want to draw edges between genes that are somehow related (co-expressed, maybe)? Is your question about how to format input for Cytoscape, or how to determine which genes are related to each other?

If that it's about Cytoscape input, then I think the simplest way is just to generate a sif file, which is a tab separated file with three columns, the first is the source node, the second is the edge type (which can be arbitrary, in a lot of cases you only have one edge type in the network, so you don't need to distinguish them), the third is the destination node.

Another simple option is just to import network data from an excel file.

You can read more about Cytoscape file formats at the Cytoscape documentation.

Answer 1

[saj98]

Hell Sean

You are right, may be my question was not clear. I am new to bioinformatic, sorry about that. Your answer very clear and useful. The issue I have, when I upload the file, I do not know how to create the edge type. This point give me the data with out connection. It is kind of boring data. Do you know how to prepare the arbitrary gene edge.

Best
Shaima

[Sean R Johnson]

Sorry for taking so long to respond. I didn't get a notification when you posted your response. Hopefully you already figured this out. If not, here's an explanation.

If I understand you correctly, your saying that when you open data in cytoscape, it only displays nodes, not edges. Try making a sif file. Here's an example:

Copy and paste the following into a text file and save it as "test.sif" or something like that

gene1 edge gene2
gene1 edge gene3
gene2 edge gene3
gene4 edge gene5
gene4 edge gene6
gene4 edge gene7

When you open cytoscape (version 3.1.1 is the one I'm using), select "From Network file..." then select test.sif, and press ok a couple times. Then you should see a network with edges. The word "edge" is totally arbitrary. You would get the same result if you had for example:

gene1   pink    gene2
gene1   green   gene3
gene2   yellow  gene3
gene4   nothing gene5
gene4   wedge   gene6
gene4   pledge  gene7

Distinguishing between different kinds of edges can be useful for some things, but it sounds like in your case it doesn't matter.

[saj98]

Hello Sean

Thank you so much for your answer, I appreciate your time.