Statistical assessment of degree of correlation seen in lncRNA-mRNA pairs defined by various criteria of relative location (“category”).

For each category, a random set of lncRNA-mRNA pairs belonging to that category was first selected, without regard to their expression profiles. Column B shows the size of this random set and Column C shows the number of members of this set for which the Pearson Correlation coefficient (PCC) in expression profiles was found to be > = 0.3. Next, we selected a random set of mRNA-mRNA pairs belonging to the category (e.g., mRNA pairs located in the same TAD if the category is “same-TAD”) as a background set; columns D and E respectively show the size of this random set of mRNA pairs and the subset thereof for which the mutual expression correlation (PCC) is > = 0.3. The latter two numbers allow us to define a baseline frequency of co-expression (PCC > = 0.3) between two genes related to each other by a particular definition (e.g., in the same TAD), which is then used to assess the statistical significance (Binomial p-value) of the number of lncRNA-mRNA pairs reported in Column C. (XLSX)