Nearby Target and Co-expression Analysis Between lncRNA and mRNA in MF vs. AMI and HF vs. MF

In order to identify nearby targeted differentially expressed mRNAs of differentially expressed lncRNAs in MF vs. AMI and HF vs. MF, the mRNAs transcribed within a 100-kb window up- or downstream of lncRNAs (19) were searched by using BEDTools (20). In addition, the Pearson correlation coefficient (cor) of lncRNAs and mRNA was calculated using the cor.test function in R. The correlation pairs with |cor| ≥ 0.98 and p-value < 0.05 were considered in that lncRNAs were significantly co-expressed with mRNAs. Interaction networks of lncRNA-nearby mRNA and lncRNA-co-expressed mRNA were visualized by using Cytoscape (21).

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