Question: Visualizing microRNA expression network
0
gravatar for Saad Khan
3.9 years ago by
Saad Khan330
United States
Saad Khan330 wrote:

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.

ADD COMMENTlink modified 3.9 years ago by Deepak Tanwar3.9k • written 3.9 years ago by Saad Khan330
2
gravatar for Deepak Tanwar
3.9 years ago by
Deepak Tanwar3.9k
ETH Zürich, Switzerland
Deepak Tanwar3.9k wrote:

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

ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by Deepak Tanwar3.9k

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)

ADD REPLYlink written 3.8 years ago by Saad Khan330
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