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Table 1 qRT-PCR validation of 20 DEGs that were similarly affected in SMK-MSC and SMK-NTC pairwise comparisons

From: Gene expression profiles associated with cigarette smoking and moist snuff consumption

  

SMK vs. MSC

SMK vs. NTC

Microarray

qRT-PCR

Microarray

qRT-PCR

Gene Symbol

Gene Name

FC

P-value (adj.)‡

FC

P-value (adj.)‡

FC

P-value (adj.)‡

FC

P-value (adj.)‡

Upregulated

 GPR15

G protein-coupled receptor 15

2.13

0

4.75

0

2.00

0

4.27

0

 LRRN3

Leucine rich repeat neuronal 3

2.07

0

2.18 a

0.0105

2.34

0

2.16 a

0.0069

 SASH1

SAM and SH3 domain containing 1

1.93

0

1.74

0

1.97

0

1.84

0

 ADAMDEC1

ADAM-like decysin 1

1.50

0.002

1.11a

0.837

1.45

0.007

1.07a

0.8469

 PID1

Phosphotyrosine interaction domain containing 1

1.37

0.013

1.27 a

0.0037

1.31

0.004

1.84 a

0

 CLEC10A

C-type lectin domain family 10, member A

1.35

0.013

1.29 a

0.0201

1.31

0.018

1.26 a

0.0041

 TMEM45B

Transmembrane protein 45B

1.31

0.047

1.1

0.7332

1.53

0.004

1.41

0.0526

 FUCA1

Fucosidase, α-L-1, tissue

1.29

0.022

1.14

0.265

1.29

0.01

1.2

0.0805

Downregulated

 PTGDS

Prostaglandin D2 synthase 21 kDa (brain)

−1.54

0.007

−2.18

0.0006

−1.86

0

−2.23

0

 PRSS23

Serine protease 23

−1.54

0.046

−1.33

0.1248

−1.98

0

−1.78

0.0152

 KLRB1

Killer cell lectinlike receptor subfamily B, member 1

−1.50

0

−1.79

0.1368

−1.47

0

−1.69

0.0041

 PTGDR

Prostaglandin D2 receptor (DP)

−1.38

0.04

−1.41

0.265

−1.55

0

−1.56

0.0391

 FYN

FYN oncogene related to SRC, FGR, YES

−1.38

0.045

−1.29a

0.5577

−1.34

0.022

−1.18 a

0.029

 NKG7

Natural killer cell group 7 sequence

−1.36

0.046

−1.51

0.0056

−1.57

0

−1.78

0.0001

 GZMA

Granzyme A (granzyme 1, cytotoxic T lymphocyte associated serine esterase 3)

−1.33

0.022

−1.30

0.5038

−1.46

0

−1.50

0.1317

 TRD

T cell receptor δ locus

−1.33

0.047

-

-

−1.57

0

-

-

 SYTL3

Synaptotagmin-like 3

−1.32

0.047

−1.19

0.1392

−1.28

0.044

−1.13

0.1654

 SEPT2

Septin 2

−1.30

0.034

−1.08

0.837

−1.26

0.033

−1.02

0.9315

 CACNA2D2

Calcium channel, voltage-dependent, α2/δ subunit

−1.28

0.033

−1.22

0.6041

−1.48

0

−2.12

0.0423

 GZMM

Granzyme M (lymphocyte metase 1)

−1.26

0.025

−1.10

0.5993

−1.36

0

−1.24

0.0805

  1. Five out of eight up-regulated genes in both SMK-MSC and SMK-NTC comparisons were confirmed by qRT-PCR. Also, seven out of 12 down-regulated genes were confirmed in SMK-NTC. In contrast, only two changes in SMK-MSC were confirmed by qRT-PCR analysis. Bolded values denote microarray changes that were confirmed by qRT-PCR. adenotes multiple qRT-PCR probes were tested but only the best result, with respect to fold change or p-value, is reported here. ‡, p-values were adjusted by FDR method for microarray experiments and by Benjamini-Hochberg method for qRT-PCR