Question: Mirna-Gene Network Construction
3
gravatar for Dataminer
7.7 years ago by
Dataminer2.6k
Netherlands
Dataminer2.6k wrote:

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.

mrna network mirna • 6.8k views
ADD COMMENTlink modified 5.8 years ago by Sasha Fokin80 • written 7.7 years ago by Dataminer2.6k

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

ADD REPLYlink written 7.7 years ago by Istvan Albert ♦♦ 80k

Ideally I want to keep miRNAs as redistribution point.

ADD REPLYlink written 7.7 years ago by Dataminer2.6k

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 REPLYlink written 7.7 years ago by Larry_Parnell16k

microRNA-gene interaction network.

ADD REPLYlink written 7.7 years ago by Dataminer2.6k
5
gravatar for Nicolas Rosewick
7.7 years ago by
Belgium, Brussels
Nicolas Rosewick7.6k wrote:

use cytoscape. It accepts a tabular entry like this :

gene1 miRNA1
gene1 miRNA2
gene2 miRNA3
gene2 miRNA4
gene2 miRNA5
...
ADD COMMENTlink written 7.7 years ago by Nicolas Rosewick7.6k

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

ADD REPLYlink written 7.7 years ago by Nicolas Rosewick7.6k
3
gravatar for Istvan Albert
7.7 years ago by
Istvan Albert ♦♦ 80k
University Park, USA
Istvan Albert ♦♦ 80k wrote:

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

ADD COMMENTlink written 7.7 years ago by Istvan Albert ♦♦ 80k
1
gravatar for Justin Brown
7.7 years ago by
Justin Brown40
Missouri, USA
Justin Brown40 wrote:

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 COMMENTlink written 7.7 years ago by Justin Brown40
1
gravatar for Sasha Fokin
5.8 years ago by
Sasha Fokin80
Russia
Sasha Fokin80 wrote:

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.

ADD COMMENTlink modified 5.3 years ago • written 5.8 years ago by Sasha Fokin80
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