Table 2.

miRanda and TargetScan score parameters can predict co-expression

Data Source	Parameter	Pearson Correlation	-log10 (P-Value)
miRanda conserved	Alignment Score	0.041	69.83
	Conservation Score	-0.023	22.16
	Free Energy	0.024	23.33
	mirSVR Score	-0.02	16.6
miRanda nonconserved	Alignment Score	0.026	139.55
	Conservation Score	-0.025	130.38
	Free Energy	-0.08	> 307
	mirSVR Score	0.024	120.49
TargetScan	Aggregate PCT	0.023	5.51
	Context Score	-0.112	141.13
	# Conserved Sites	0.0299	9.61
	# Nonconserved Sites	-0.064	45.92
	# Conserved 7mer-1a sites	0.019	3.27
	# Conserved 7mer-m8 sites	0.014	1.39
	# Conserved 8mer sites	0.02	4.2
	# Nonconserved 7mer-1a sites	-0.094	99.64
	# Nonconserved 7mer-m8 sites	0.031	10.64
	# Nonconserved 8mer sites	-0.008	0

For each predicted miRNA-mRNA pair from the miRanda conserved, miRanda nonconserved, and TargetScan datasets, the Pearson correlation coefficient for co-expression across multiple RNA-seq experiments was obtained. The correlation coefficient was then compared to various predictor variables provided by miRanda/TargetScan, across all pairs, again using Pearson correlation. (P-values after Bonferroni correction; * indicates significance at p < 0.05; ** indicates significance at p < 0.001).