Table 2. Altered transcript expression in PDTC samples as compared to benign counterparts.

Gene	P-value (PDTC vs benign)	P-value with FDR (PDTC vs benign)	Fold change	Total number of samples PDTC/benign	Number of samples with expression value > 50 (linear scale) PDTC/benign
1. Without consideration of PDTC type
BCL2	0.0000	0.0000	−2.63	25/22	25/22
CDKN1B	0.0093	0.0158	−3.68	25/22	24/22
CHEK1	0.0000	0.0000	25.14	25/22	25/10
CRY2	0.0000	0.0000	−2.07	25/22	25/22
DIO2	0.0001	0.0001	−3.10	25/22	25/22
FZD1	0.0000	0.0001	−2.68	25/22	25/22
KDR	0.0000	0.0000	−3.68	25/22	25/22
c-KIT	0.0002	0.0004	−9.98	25/22	19/22
PER2	0.0000	0.0000	−3.06	25/22	25/22
SLC26A4	0.0000	0.0000	−17.79	25/22	22/22
SLC5A5	0.0000	0.0000	−29.94	25/22	16/19
TG	0.0000	0.0000	−10.60	25/22	24/22
TPO	0.0000	0.0000	−28.68	25/22	23/22
2. Non-oncocytic PDTC
CHEK1	0.0000	0.0000	20.96	15/22	15/10
DIO2	0.0086	0.0188	−2.29	15/22	15/22
KDR	0.0000	0.0000	−2.69	15/22	15/22
SLC26A4	0.0001	0.0005	−10.99	15/22	14/22
SLC5A5	0.0003	0.0011	−23.77	15/22	10/19
TG	0.0002	0.0009	−4.58	15/22	15/22
TPO	0.0000	0.0000	−17.02	15/22	14/22
3. Oncocytic PDTC
BCL2	0.0000	0.0000	−5.37	10/22	10/22
CDKN1B	0.0057	0.0096	−5.97	10/22	9/22
CHEK1	0.0000	0.0000	33.02	10/22	10/10
CRY2	0.0000	0.0000	−3.38	10/22	10/22
DIO2	0.0000	0.0000	−4.87	10/22	10/22
FZD1	0.0000	0.0000	−5.53	10/22	10/22
KDR	0.0000	0.0000	−5.90	10/22	10/22
c-KIT	0.0000	0.0000	−43.36	10/22	6/22
PER2	0.0000	0.0000	−6.46	10/22	10/22
SLC26A4	0.0000	0.0000	−36.62	10/22	8/22
SLC5A5	0.0002	0.0003	−42.32	10/22	6/19
TG	0.0000	0.0000	−37.29	10/22	9/22
TPO	0.0000	0.0000	−62.72	10/22	9/22