Analysis of lncRNA-mRNA Co-expression

Firstly, we used genome annotation and genome browser to screen mRNAs with differential expression in the upstream and downstream of lncRNAs in the range of 10 kb. Then, Pearson correlation method was used to analyze the correlation between these lncRNAs and mRNAs expression levels. The mRNAs with correlation may be the lncRNA cis regulated genes. Subsequently, for mRNAs not in the range(10 kb), Pearson correlation method was also used to analyze the correlation of their expression. These correlated mRNAs may be lncRNA trans regulated genes. All correlated mRNAs are also known as lncRNA co-expressed mRNAs. The criteria for correlation screening were Pearson’s correlation coefficient ≥0.9 and p-value < 0.5. The obtained lncRNAs and mRNAs were constructed in a co-expression network of lncRNAs and mRNAs visualized using Cytoscape software v3.9.0.