Table 3 Quantification Reliability of Short Amplicons in FFPE tissue

RNA		Short-A amplicon			Short-B amplicon			Short-C amplicon			Correlation
P value			Fold change*		P value	Fold change*		P value	Fold change*		2 amplicons	3 amplicons
DD3	Dukes' A	0.519	1.2	0	0.507	2.3	0	0.035	2.5	Up	+	-
	Dukes' B	0.038	0.8	0	0.647	1.7	0	0.019	2.3	Up	+	-
H19	Dukes' A	0.000	14.7	Up	0.000	12.6	Up	0.000	3.5	Up	+	+
	Dukes' B	0.000	13.8	Up	0.000	61.8	Up	0.000	7.6	Up	+	+
MALAT1	Dukes' A	0.874	1.0	0	0.175	0.9	0	0.000	0.6	0	+	+
	Dukes' B	0.001	0.6	0	0.001	0.6	0	0.038	0.9	0	+	+
MEG3	Dukes' A	0.258	0.8	0	0.041	0.6	0	0.016	0.8	0	+	+
	Dukes' B	0.231	1.0	0	0.228	0.8	0	0.056	0.9	0	+	+
p15AS	Dukes' A	0.001	2.5	Up	0.035	1.7	0	0.001	2.0	Up	+	-
	Dukes' B	0.004	1.3	0	0.018	2.1	Up	0.011	2.4	Up	+	-
UCA1	Dukes' A	0.000	10.0	Up	0.000	11.2	Up	0.000	8.5	Up	+	+
	Dukes' B	0.000	5.6	Up	0.000	8.2	Up	0.000	7.0	Up	+	+
CDK6	Dukes' A	0.003	2.1	Up	0.002	3.7	Up	0.009	1.8	0	+	-
	Dukes' B	0.040	1.5	0	0.047	1.7	0	0.143	1.4	0	+	+
JUN	Dukes' A	0.308	0.8	0	0.003	0.7	0	0.000	0.5	Down	+	-
	Dukes' B	0.006	0.7	0	0.000	0.4	Down	0.000	0.5	Down	+	-
MAPK3	Dukes' A	0.041	0.8	0	0.000	0.5	Down	0.001	0.7	0	+	-
	Dukes' B	0.011	0.8	0	0.000	0.5	Down	0.058	0.7	0	+	-
PDGFRA	Dukes' A	0.001	0.7	0	0.000	0.6	0	0.026	0.9	0	+	+
	Dukes' B	0.000	0.6	0	0.000	0.8	0	0.006	0.7	0	+	+
PDGFRB	Dukes' A	0.000	1.7	0	0.001	2.1	Up	0.000	2.3	Up	+	-
	Dukes' B	0.003	1.1	0	0.001	1.4	0	0.000	2.2	Up	+	-
PIK3R3	Dukes' A	0.005	2.6	Up	0.031	1.4	0	0.000	2.5	Up	+	-
	Dukes' B	0.002	1.3	0	0.129	1.2	0	0.000	1.6	0	+	+
SMAD3	Dukes' A	0.717	1.1	0	0.091	0.9	0	0.914	1.1	0	+	+
	Dukes' B	0.681	0.6	0	0.006	0.7	0	0.943	1.1	0	+	+
SMAD4	Dukes' A	0.993	1.0	0	0.948	1.2	0	0.235	1.3	0	+	+
	Dukes' B	0.071	0.9	0	0.008	0.8	0	0.102	0.6	0	+	+
Correlation											100%	57%

*, tumour/normal tissue; +, correlated; -, uncorrelated; Up, Up-regulated; Down, down-regulated; 0, unchanged.

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