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.
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Dataminer
use cytoscape. It accepts a tabular entry like this :
gene1 miRNA1
gene1 miRNA2
gene2 miRNA3
gene2 miRNA4
gene2 miRNA5
...
and you can even give a weight for each interaction. Just specify in the tab file a third colum with the weight ;)
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
If you are looking for tools to visualize graphs, I have found that Graphviz makes nice looking graphs. See the gallery for some examples.
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.
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What are your definitions for the nodes and edges of the network?
Ideally I want to keep miRNAs as redistribution point.
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?
microRNA-gene interaction network.