Visualizing microRNA expression network

Question

[Saad Khan]

Hi All,

I have a list of differentially expressed microRNA (using edgeR GLM model) which I have compared to different tissues.Now I want to visualize these for possible interactions and ontology enrichment. What could be the possible way forward. I know there exists mirScape but it probably does not have a lot of functionality. I want to color code these miRNAs according to their expression/p-value. Kindly let me know what could be the best way forward to produce publication quality graphics for the same.

Answer 1

[Deepak Tanwar]

use R.

There are number of R packages, which can help you for GO enrichment analysis.

Search for packages on http://www.bioconductor.org.

Plot with ggplot2 http://www.statmethods.net/advgraphs/ggplot2.html

[Saad Khan]

Most of these packages are meant for RNA-seq data. I am talking about small-RNA-seq or miRNA-seq data. Also I want to visualize the role of these microRNA on a Pathway and for that bioconductor is not a good option IMHO. I am not so adept at using Cytoscape although there are packages in cytoscape like cytragetlinker (http://projects.bigcat.unimaas.nl/cytargetlinker/tutorial-1/#step1) which seem to fail to work with a small list of microRNAs (5)