Question

Mirna-Gene Network Construction

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13.3 years ago

Dataminer ★ 2.8k

Hi!

I have a genelist (167 genes) and these genes contain motifs for 6 miRNA (some of these genes may be contain motif for than one miRNA's).

I want to construct a network representing interaction between these genes-miRNA's and between miRNA's as well.

Any suggestions?

Thank you in advance.

mirna mrna network • 9.1k views

ADD COMMENT • link updated 11.4 years ago by Sasha Fokin ▴ 80 • written 13.3 years ago by Dataminer ★ 2.8k

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What are your definitions for the nodes and edges of the network?

ADD REPLY • link 13.3 years ago by Istvan Albert 102k

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Ideally I want to keep miRNAs as redistribution point.

ADD REPLY • link 13.3 years ago by Dataminer ★ 2.8k

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Fine. But do you wish to show gene-gene interactions and if so, are those interactions physical (protein-protein) or genetic? Or are you only interested in microRNA-gene interactions?

ADD REPLY • link 13.3 years ago by Larry_Parnell 16k

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microRNA-gene interaction network.

ADD REPLY • link 13.3 years ago by Dataminer ★ 2.8k

score 5 · Answer 1 · 2011-09-05

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13.3 years ago

Nicolas Rosewick 11k

use cytoscape. It accepts a tabular entry like this :

gene1 miRNA1
gene1 miRNA2
gene2 miRNA3
gene2 miRNA4
gene2 miRNA5
...

ADD COMMENT • link 13.3 years ago by Nicolas Rosewick 11k

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and you can even give a weight for each interaction. Just specify in the tab file a third colum with the weight ;)

ADD REPLY • link 13.3 years ago by Nicolas Rosewick 11k

score 3 · Answer 2 · 2011-09-03

Building a network is a fairly straightforward matter. You will need to define what is a node in your network and then define the condition by which to consider two nodes to be connected (form an edge).

Then, all you need is to create a file in a simple file text format like GML or an XML based format GraphML. You may generate these with various tools that usually will also allow you to compute certain network properties. Finally you can visualize your network with network drawing tools

score 1 · Answer 3 · 2011-09-07

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13.3 years ago

Justin Brown ▴ 40

If you are looking for tools to visualize graphs, I have found that Graphviz makes nice looking graphs. See the gallery for some examples.

ADD COMMENT • link 13.3 years ago by Justin Brown ▴ 40

score 1 · Answer 4 · 2013-08-15

Hi, dataminer!

We are now building a similar database and online dataviz tool on cytoscape web -- MirOB (MicroRNA OncoBase).

Database includes validated microRNAs and Transcription Factors Targets associated with human cancers. More 6500 interactions with special emphasize on the specific types of cancer, pathological processes and expression level alterations. Currently, MirOB supports only homo sapiens organism.

You can try our simple tool here.

If the information is open, could you give us a list of genes and miRNA of interest to you. We would like to test our tools.