Software for gene co-expression network analysis / clustering enabling integration of paired miRNA-mRNA expression data

Question

[lech.kaczmarczyk]

Hi All ! I have miRNA and mRNA expression data from 3 different cell types, each 4 + 4 (miRNA and mRNA) replicates. Is there a software enabling integration of such data, to do gene (co-expression) network construction and pathway analysis? I found tools galore, but (quite surprisingly) nothing really allows for pairing miRNA and mRNA coming from the same samples (or I failed to see such functionality). Of course individual tools may be coupled together to tailor a suitable workflow, but I want to make sure I'm not re-inventing a wheel. Any tips will be appreciated! Cheers, Lech

[Kevin Blighe]

It depends on how you have processed your data. If you have processed it together, then there's nothing stopping you from using any type of network analysis because the miRNA and mRNA data will be measured on the same scale and processed in the same way.

A former colleague of mine implemented miRNA and mRNA integration via network analysis but via MatLab. Not sure if that is of any use: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003676

Apart from that, why not just see if your miRNAs are predicted targets of your mRNAs and then construct 'custom' networks showing a connection between a particular mRNA and one or more miRNAs (if on such connection exists). I have done this previously.