any tool or R package for integrated analysis of miRNA and mRNA expression data ??

Question

[unique379]

Hello guys,

I need any tool or packages for integrated analysis of miRNA and mRNA expression data? More specific I have time course expression data from microarray experiment.

Thanks in advance

Answer 1

[Irsan]

It depends on your definition of integrated analysis. The most simple (and also least powerful) way of integration is to do differential analysis on mRNA and miRNA between your timepoints seperately and afterwards compare the differential results. You can look if annotated mRNA-miRNA pairs according to the miranda database change over time in opposite directions. However, a much more powerful approach is to use regression of miRNA on mRNA expression estimates to look for significant negative interactions between any miRNA-mRNA pair. You don't need a special package, linear regression is in the base functionality of R. The advantage of the latter approach is explained by the following example. Supposed you have a set of 50 control and 60 tumor samples. In all samples, the miRNA expression and mRNA expression, which are known to be interacting, are similar except for 1 tumor. This tumor has low expression of the mRNA and high expression of the miRNA. So you see silencing of the gene that is most likely caused by the increased expression of the miRNA. With regression analysis you will find this very easily. However if you did differential expression analysis between tumor and control, both miRNA and mRNA would not have been significant because the one tumor sample does not make the means of the tumor and control cohorts different.

[Kristoffer Vitting-Seerup]

Nice idea! To model the interactions more dicretly (trying to remove indirect effects) do you know of a way to contrain that positive effects should not be considered aka only looking for negative effects?

[Kristoffer Vitting-Seerup]

Btw is the miranda database still maintained (or even available?). Alternatively there are other large databases such mirbase and mirgenedb as and finally mirTarDb which is smaller but experimentally validated.

Answer 2

[k.beats]

There seem to be quite a few tools out there capable of integrative miRNA-mRNA analysis. This one seems quite comprehensive: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4696828/

Answer 3

[andrew.j.skelton73]

I haven't seen anything that will generically do that kind of analysis. You might consider an eQTL analysis of sorts maybe?

[Diwan]

Just curious, have you come across any tutorial or paper that do such integrated miRNA/mRNA analyses?

[andrew.j.skelton73]

to be clear, are you talking about mRNA gene expression data, and miRNA Sequencing?

[Diwan]

I am new to the topic and was curious to see some exemplar works (whichever the standard approach is). But when I googled the topic I find there are many papers on the topic. Sorry, I should have googled first :( before asking query.

Answer 4

[Kristoffer Vitting-Seerup]

There seems to be 12 R packages for miRNA analysis annotated in Bioconductor - maybe one of those?