Does anyone have suggestions for linking a list of lncRNAs to their target mRNAs? I am looking to generate networks consisting of lncRNA-mRNAs that are activated or downregulated in response to a particular intervention (as identified by microarray analysis). Thanks.
John Hardy Lockhart
Predicting direct interactions between lncRNAs and mRNA is not currently feasible from sequencing data. However, you could try to use gene module analysis to genes that are co-expressed which might imply some direct interaction or shared regulatory mechanisms. (See this review Article A comprehensive evaluation of module detection methods for g...
) One thing to keep in mind, is that the modules constructed from these analyses may be statistically significant without any true biological significance, so the outputs still need to be verified by targeted molecular biology techniques (e.g. qRT-PCR).
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