Figure 1. The flowchart of lncRNA-associated PPI module identification For a given lncRNA and mRNA expression profiles, the correlations between each pair (lncRNA and mRNA) were measured using the Spearman’s correlation coefficient (SCC).

The co-expressed mRNAs were then determined using the mutual correlation rank score (MR), the geometric average of the absolute value of SCC (|SCC|) rank from lncRNA to mRNA and vice versa. For each lncRNA, the top-scoring mRNAs were selected as the co-expressed mRNAs (lncRNA-associated mRNAs). Subsequently we used protein-protein interaction analysis of co-expression mRNAs to find lncRNA-associated PPI modules. Finally, we performed gene ontology enrichment analysis on the associated mRNAs of each lncRNA module to understand their regulatory functions.