Clustering Analysis In Gene Coexpression Network

Question

[Ane]

Hello!

I have a gene coexpression network and i want to analyse and visualize the clusters of the network (i.e show different clusters in different colours). I have used R studio and cytoscape for the network construction and analysis, so far. Although i have managed to define the modules of the network with different algorithms, i couldn't find a proper way to visualize the clusters. Cytoscape plugins Glay and ClusterMaker seemed very helpful but unfortunately they are not compatible with cytoscape 2.8.

Could you recommend similar cytoscape plugins, r packages and/or any other software for this kind of analysis?

Thanks in advance, Ane

[Neilfws]

"used R studio" - Rstudio is an R IDE, so this does not tell us what you did. Did you use an R package?

[Ane]

yes, i used igraph and i have imported it into cytoscape with graphml plugin

Answer 1

[Arnaud Ceol]

I'm using ClusterMaker with Cytoscape 2.8 without problem. Once you have created the cluster, a button appears allowing you to visualize them.

[Ane]

i was trying to install a previous version! i created the clusters with mcl algorithm and managed to visualize them, too! Is there any way to visualize them in different colours in the same network?

[Arnaud Ceol]

The answer comes quite late, but maybe it still can be useful for someone. When you create the clusters, there is an advanced Cytoscape option to generate metanodes. An attribute will be added to each node that you can use to colour the clusters.

Answer 2

[Leandro Lima]

Hello, Ane!

Maybe this post can help you.

gene coexpression networks