Table 5. Altered transcript expression in PTC versus benign samples (combined PTC samples).

Gene	P-value (PTC vs benign)	P-value with FDR (PTC vs benign)	Fold change	Total number of samples	Number of samples with expression value > 50
Without consideration of clinical aggressiveness
BCL2	1.86 × 10−6	1.42 × 10−5	−2.21	58	58
BMAL1	3.15 × 10−6	1.42 × 10−5	2.87	58	58
CHEK1	5.48 × 10−6	1.97 × 10−5	2.97	58	56
c-KIT	2.43 × 10−6	1.42 × 10−5	−5.64	58	56
c-MET	5.41 × 10−8	9.74 × 10−7	3.48	58	58
PPARγ	1.64 × 10−3	2.95 × 10−3	−2.55	58	54
TG	6.38 × 10−4	1.28 × 10−3	−2.39	58	58
TIMP1	1.34 × 10−5	3.45 × 10−5	3.39	58	58
ALDH1	2.66 × 10−3	1.97 × 10−2	−2.55	32	32
VDR	2.38 × 10−3	2.11 × 10−2	3.15	26	25
With consideration of clinical aggressiveness: more aggressive PTC (group II in Tables 1,2)
BCL2	2.33 × 10−9	2.10 × 10−8	−2.70	45	45
BMAL1	1.15 × 10−7	3.46 × 10−7	3.49	45	45
CHEK1	9.81 × 10−6	2.21 × 10−5	3.10	45	43
c-KIT	7.07 × 10−8	2.55 × 10−7	−7.82	45	43
c-MET	1.30 × 10−12	2.35 × 10−11	4.81	45	45
PPARγ	2.30 × 10−5	4.60 × 10−5	−3.56	45	41
TG	2.03 × 10−7	5.22 × 10−7	−3.52	45	45
TIMP1	2.05 × 10−8	9.24 × 10−8	4.79	45	45
ALDH1	2.63 × 10−4	2.30 × 10−3	−3.26	25	25
DIO2	2.24 × 10−2	4.23 × 10−2	−2.41	25	25
VDR	2.85 × 10−3	2.28 × 10−2	3.36	20	19

41 PTC samples enrolled in the study (17 PTC samples from the first cohort (Table 1), and 24 PTC from the second cohort (Table 2)) were compared to 17 benign nodules from the first cohort (Table 1).