Can I perform ceRNA network analysis when I have only lncRNA and mRNA data?
My RNA-seq data only contains lncRNA and mRNA expression profile; I see many package support ceRNA analysis but require expression profile of miRNA. I suppose the miRNA can be predicted in databases, but don't know which R package can exactly do this. Can anyone help me with this?
Hi
miRNA expression also needs to get from the experiments. You can predict miRNAs from gene lists or from the lncRNA target but not the expression values. Some people get the miRNA expression data by using mRNA sequencing and annotation but it is not a suitable way.
To construct the network, you might predict miRNA firstly then using the list of predicted miRNAs to identify the ceRNAs
best
Sure. Just calculate the correlation between mRNAs and lncRNAs, and then use miRNAs to connect them, such as sharing high proportion of miRNAs or even just share a miRNA.
You need some miRNA target databases, such as targetScan or mirTarBase, to obtain the interactions between miRNAs and mRNA/lncRNA.
For the correlation between RNAs, the command 'corr' in R works.
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