|
QPCR validation experiment
| | | | | | | | | | |
|---|
| |
Normalized relative expressiona
| | |
Fold change and P-value Student’sT-testb
| |
|---|
| |
NS (n = 10)
|
AK (n = 13)
|
SSC (n = 15)
|
SCC vs NS
|
AK vs NS
|
SCC vs AK
|
|---|
|
Gene
|
Median
|
SE
|
Median
|
SE
|
Median
|
SE
|
log2(FC)
|
p-value
|
log2(FC)
|
p-value
|
log2(FC)
|
p-value
|
|---|
|
CCL27
|
18,45
|
2,53
|
2,46
|
0,91
|
0,11
|
0,14
|
−7,34
|
5,48E-05
|
−2,91
|
1,80E-04
|
−4,43
|
3,30E-03
|
|
KRT17
|
0,12
|
0,03
|
1,19
|
0,41
|
5,20
|
0,97
|
5,39
|
7,13E-05
|
3,26
|
7,07E-03
|
2,13
|
1,13E-03
|
|
MMP1
|
0,01
|
0,01
|
0,28
|
1,16
|
47,19
|
35,2
|
12,18
|
5,68E-02
|
4,80
|
2,32E-01
|
7,38
|
6,14E-02
|
|
MMP3
|
0,01
|
0,01
|
0,36
|
0,37
|
17,91
|
4,95
|
10,99
|
3,03E-03
|
5,36
|
4,07E-02
|
5,63
|
4,31E-03
|
|
MMP9
|
0,07
|
0,01
|
1,83
|
0,74
|
4,49
|
4,21
|
6,07
|
1,82E-02
|
4,77
|
4,42E-03
|
1,30
|
6,07E-02
|
|
MMP10
|
0,02
|
0,03
|
0,95
|
1,17
|
17,70
|
8,24
|
9,59
|
2,69E-03
|
5,38
|
4,53E-02
|
4,21
|
5,16E-03
|
|
PI3
|
0,02
|
0,01
|
2,01
|
1,67
|
10,62
|
6,23
|
8,95
|
5,46E-03
|
6,55
|
7,71E-03
|
2,40
|
3,25E-02
|
|
SERPINB4
|
0,004
|
0,002
|
1,99
|
6,2
|
18,79
|
15,7
|
12,33
|
2,35E-02
|
9,09
|
3,96E-02
|
3,24
|
1,46E-01
|
|
TUBB3
|
0,51
|
0,08
|
0,64
|
0,17
|
3,68
|
0,94
|
2,85
|
1,17E-03
|
0,32
|
3,20E-01
|
2,53
|
1,78E-03
|
|
Genome-wide expression analysis
| | | | | | | | | |
| |
Normalized expression
c
| | | |
Results limma analysis
| | | |
| |
NS (n = 13)
|
AK (n = 14)
|
SSC (n = 15)
|
SCC vs NS
|
AK vs NS
|
SCC vs AK
|
|
Gene
|
Median
|
SE
|
Median
|
SE
|
Median
|
SE
|
log
2
FC
|
Adj. p-val
|
log
2
FC
|
Adj. p-val
|
log
2
FC
|
Adj. p-val
|
|
CCL27
|
12,92
|
0,02
|
10,74
|
0,10
|
8,60
|
0,03
|
−4,24
|
2,03E-15
|
−2,24
|
9,64E-08
|
−2,00
|
1,65E-06
|
|
KRT17
|
10,58
|
0,07
|
14,43
|
0,10
|
15,56
|
0,01
|
4,84
|
1,28E-14
|
3,16
|
5,56E-09
|
1,68
|
3,66E-04
|
|
MMP1
|
8,32
|
0,00
|
8,39
|
0,05
|
10,80
|
0,08
|
2,41
|
5,70E-10
|
0,22
|
5,65E-01
|
2,20
|
1,61E-07
|
|
MMP3
|
8,33
|
0,01
|
8,55
|
0,06
|
10,59
|
0,08
|
2,44
|
1,16E-09
|
0,50
|
1,59E-01
|
1,84
|
6,86E-06
|
|
MMP9
|
8,48
|
0,01
|
9,29
|
0,06
|
10,50
|
0,09
|
2,22
|
1,37E-07
|
1,05
|
8,50E-03
|
1,93
|
2,02E-06
|
|
MMP10
|
8,31
|
0,00
|
8,33
|
0,02
|
10,02
|
0,10
|
1,93
|
3,07E-07
|
0,09
|
8,41E-01
|
1,16
|
4,61E-03
|
|
PI3
|
9,16
|
0,05
|
13,60
|
0,14
|
15,27
|
0,04
|
5,68
|
1,33E-13
|
3,96
|
1,09E-08
|
1,72
|
3,44E-03
|
|
SERPINB4
|
8,34
|
0,02
|
10,22
|
0,13
|
12,04
|
0,10
|
3,81
|
5,15E-09
|
2,16
|
3,64E-04
|
1,65
|
6,04E-03
|
|
TUBB3
|
8,84
|
0,01
|
8,86
|
0,05
|
10,45
|
0,05
|
1,91
|
5,45E-11
|
0,23
|
3,66E-01
|
1,67
|
5,28E-08
|
-
a Relative expression normalized to the expression level of four reference genes.
-
b Bold values represent the comparisons that could be statistically confirmed in the QPCR validation experiment.
-
c VST transformed RSN normalized data.
