Table 3

List of 178 genes that show significant "Tissue * Storage" interaction and are also differentially expressed in breast cancer tissue at FDR 0.05 level with at least 1.4 fold change in the combined analysis.

GENE_SYMBOL

p-value (Disease)

p-value (Storage)

p-value (Case ID)

p-value (Disease * Storage)

Fold- Change (Tumor vs. Normal)

Fold-Change (FFPE vs. FF)


WRB

1.78E-03

3.40E-09

7.35E-07

6.59E-06

-1.41

-2.21


TPCN1

1.10E-05

8.55E-01

4.37E-05

6.85E-06

1.66

1.02


ANKFY1

1.95E-06

7.64E-01

1.04E-04

7.24E-06

1.42

1.02


CYP2U1

2.62E-08

8.80E-10

1.16E-03

1.01E-05

-1.98

-2.22


SMTN

9.55E-04

1.47E-01

2.11E-04

1.24E-05

1.47

1.17


LNX1

2.10E-05

7.85E-04

3.50E-02

1.30E-05

-1.90

-1.62


CBL

2.48E-05

8.60E-06

2.30E-05

1.71E-05

-1.62

-1.68


KLHL2

9.67E-04

1.51E-10

2.73E-07

1.72E-05

-1.46

-2.57


AKAP8L

1.75E-07

1.64E-01

6.17E-04

1.87E-05

1.75

1.13


RFXANK

1.13E-07

3.60E-01

9.57E-05

2.32E-05

1.65

1.07


CTBP1

1.41E-06

6.11E-05

7.37E-06

2.94E-05

1.54

1.40


HELB

7.51E-08

6.99E-06

3.10E-03

3.78E-05

2.89

2.28


CCDC101

5.10E-05

7.93E-01

1.24E-02

4.39E-05

1.51

-1.02


SFRS16

6.63E-04

7.91E-05

2.77E-02

4.66E-05

1.58

-1.73


C2orf33

1.98E-03

5.92E-02

5.27E-11

4.77E-05

-1.41

-1.22


SMARCB1

7.18E-10

1.10E-02

2.94E-04

5.15E-05

1.81

1.21


TOLLIP

4.00E-07

9.39E-02

9.85E-05

5.16E-05

2.58

1.30


PLEC1

4.76E-06

1.18E-09

3.41E-05

6.28E-05

1.71

2.26


EBNA1BP2

2.76E-05

5.97E-03

4.00E-05

6.47E-05

1.41

-1.23


EFTUD2

4.09E-06

1.28E-03

6.33E-02

6.59E-05

1.40

1.24


POLDIP3

1.58E-07

2.39E-01

6.11E-03

8.18E-05

1.44

1.07


RPL6

1.21E-10

3.21E-04

6.06E-04

8.22E-05

2.53

1.51


ITIH5

4.60E-05

6.68E-01

1.87E-02

8.39E-05

-1.56

1.04


GBF1

1.18E-08

4.35E-03

1.05E-03

1.00E-04

1.97

1.32


MAEA

2.50E-08

4.61E-02

7.21E-02

1.03E-04

1.68

1.16


CCT2

1.17E-08

6.92E-05

2.15E-04

1.15E-04

1.71

1.39


SMC6

5.61E-04

4.28E-03

1.65E-05

1.31E-04

-1.51

-1.40


C19orf61

8.87E-08

4.16E-01

2.55E-02

1.31E-04

1.99

1.09


VPS28

1.63E-06

1.44E-01

7.92E-04

1.34E-04

1.62

-1.13


QTRT1

2.39E-04

4.20E-01

8.43E-01

1.37E-04

1.60

1.10


RPL12

5.18E-06

1.54E-01

4.17E-02

1.40E-04

1.49

-1.11


CNOT3

4.87E-07

9.43E-01

1.48E-03

1.43E-04

1.72

-1.01


BANF1

7.48E-09

1.49E-03

1.84E-04

1.51E-04

1.57

1.23


AATF

1.92E-07

8.25E-02

1.08E-03

1.58E-04

1.76

-1.17


NDUFAF1

2.59E-05

8.26E-11

1.35E-01

1.60E-04

-1.49

-2.12


SDCCAG1

2.36E-05

1.39E-01

3.91E-04

1.69E-04

1.50

-1.13


BNIP1

2.36E-05

5.09E-04

5.73E-03

1.72E-04

1.53

1.39


LOC728758

3.19E-04

1.24E-02

6.97E-03

1.74E-04

-1.82

1.49


RPL23AP7

1.52E-06

5.66E-10

1.00E-01

1.79E-04

1.41

-1.65


LSM11

7.45E-07

5.36E-01

1.06E-02

1.87E-04

1.58

1.05


CLPTM1

3.20E-06

6.03E-04

1.21E-04

1.88E-04

1.58

1.37


POGZ

8.70E-05

5.28E-07

2.38E-02

1.91E-04

1.48

1.71


SC5DL

7.77E-07

3.64E-02

2.47E-08

2.02E-04

-1.61

1.19


XRCC6

9.50E-07

6.25E-01

4.42E-03

2.13E-04

1.83

1.05


LOC205251

7.83E-04

2.26E-04

5.18E-03

2.41E-04

1.57

-1.66


PLEKHG1

1.89E-06

5.93E-05

2.48E-04

2.42E-04

-2.18

-1.87


SPATA22

1.33E-05

1.92E-02

4.97E-04

2.48E-04

-2.62

-1.60


CENTB5

5.14E-05

7.22E-02

5.84E-04

2.54E-04

1.67

1.23


ZCCHC8

8.69E-06

1.74E-02

1.17E-02

2.67E-04

1.47

1.20


KLHL20

4.97E-06

9.02E-02

5.65E-01

2.77E-04

-1.62

1.17


BANK1

2.22E-08

3.82E-05

6.06E-03

2.93E-04

-2.95

-2.03


SGTA

3.52E-04

5.78E-02

3.09E-04

2.93E-04

1.57

-1.25


ACIN1

1.88E-05

4.24E-10

4.33E-03

2.98E-04

1.45

1.91


RCE1

2.27E-08

3.07E-05

4.81E-03

3.16E-04

1.81

1.49


NUDT13

1.37E-05

2.79E-06

4.24E-04

3.33E-04

-1.45

-1.51


GPR64

4.44E-09

1.13E-04

1.69E-03

3.33E-04

-2.75

-1.77


STAMBPL1

4.63E-04

1.47E-05

1.28E-01

3.44E-04

-1.41

-1.56


SHKBP1

2.42E-06

1.23E-07

8.23E-04

3.71E-04

1.49

1.60


C9orf86

2.04E-05

6.48E-01

1.82E-03

3.81E-04

2.40

-1.09


ECHDC1

2.80E-06

3.82E-03

2.11E-06

3.88E-04

-2.04

-1.49


EDF1

5.10E-06

2.30E-01

8.34E-05

4.12E-04

1.42

1.08


PRMT7

2.10E-04

8.12E-01

6.42E-03

4.12E-04

2.11

1.04


HERC2P2

7.56E-04

9.75E-03

6.71E-01

4.36E-04

1.85

1.58


TOPORS

1.21E-04

2.75E-06

1.66E-06

4.37E-04

-1.64

-1.90


RCBTB2

1.80E-04

2.21E-06

1.76E-05

4.38E-04

-1.53

-1.77


BRF1

4.92E-06

5.96E-02

5.32E-05

4.40E-04

1.92

1.26


LOC440836

2.48E-04

3.96E-09

2.34E-04

4.45E-04

2.13

4.21


ZNF800

2.21E-03

4.28E-06

1.26E-05

4.48E-04

-1.46

-1.87


IGBP1

3.76E-04

1.23E-04

7.30E-02

4.62E-04

1.77

1.87


SLCO1C1

7.65E-11

1.40E-05

7.92E-06

4.71E-04

-2.18

-1.53


CCDC97

2.50E-05

2.67E-04

2.14E-02

4.73E-04

1.65

-1.52


ARMCX1

2.36E-05

1.27E-05

6.04E-06

5.06E-04

-1.87

-1.92


PCAF

6.56E-06

2.64E-09

7.50E-05

5.09E-04

-1.53

-1.89


INPP5A

1.98E-03

1.20E-03

4.68E-04

5.26E-04

-1.45

-1.48


FGFR1OP2

1.03E-04

2.73E-03

5.53E-05

5.32E-04

-1.47

-1.33


ZBTB37

1.07E-03

8.73E-01

3.47E-05

5.33E-04

1.61

-1.02


ERGIC1

5.17E-07

1.05E-02

1.77E-02

5.42E-04

1.64

-1.24


THAP10

3.18E-04

1.96E-03

2.71E-02

5.62E-04

-1.70

-1.56


CSTF2T

1.64E-03

2.02E-10

3.38E-05

5.71E-04

-1.55

-3.08


CTNND1

1.96E-06

5.30E-05

2.25E-01

5.72E-04

1.49

1.38


CKS2

2.43E-05

9.21E-04

2.19E-01

5.73E-04

2.73

-2.11


C7orf26

1.34E-04

4.08E-01

5.39E-02

5.75E-04

1.55

1.09


PRKAR1B

6.89E-04

1.47E-01

1.68E-01

5.79E-04

1.76

1.25


NF2

8.23E-08

1.54E-01

8.02E-03

5.88E-04

1.60

1.11


UBR4

2.48E-05

9.60E-08

5.01E-02

6.22E-04

1.53

1.80


UFM1

2.30E-05

5.45E-01

4.26E-09

6.36E-04

-1.45

-1.05


ARID1B

1.38E-03

1.01E-03

5.96E-01

6.39E-04

1.43

1.44


TSPAN12

7.09E-06

1.31E-07

2.74E-06

6.41E-04

-2.17

-2.63


TXNDC5

4.99E-08

2.44E-08

6.66E-04

6.45E-04

1.77

1.81


CLTC

9.24E-05

7.98E-11

3.76E-04

6.57E-04

-1.45

-2.16


C17orf38

1.38E-03

1.16E-01

3.79E-01

6.58E-04

1.84

1.33


SHOC2

3.10E-04

3.40E-08

9.38E-03

6.73E-04

-1.46

-1.94


MAN2B1

1.59E-04

1.04E-04

1.87E-02

6.88E-04

1.47

1.49


FUCA2

3.16E-04

1.16E-03

1.02E-02

6.92E-04

-1.74

-1.63


MED24

4.68E-07

7.29E-01

1.60E-03

7.36E-04

1.82

-1.03


C1orf86

2.05E-08

8.20E-02

2.70E-05

7.73E-04

1.85

-1.16


TUBGCP6

2.57E-05

2.13E-02

1.35E-02

7.77E-04

1.47

1.21


PLCB3

3.60E-05

1.98E-02

3.19E-02

7.84E-04

1.50

-1.23


PAN3

1.27E-05

3.57E-09

1.41E-04

7.84E-04

-1.44

-1.75


BDH2

8.19E-06

1.98E-06

6.92E-03

7.87E-04

-2.50

-2.71


NR3C2

6.25E-07

2.97E-11

1.65E-03

7.93E-04

-2.29

-3.68


TRIM44

1.74E-04

2.28E-03

9.50E-03

8.03E-04

-1.80

-1.59


RBM42

3.45E-08

8.38E-01

1.16E-04

8.14E-04

1.40

-1.01


IQCB1

1.52E-06

7.01E-04

5.37E-03

8.21E-04

1.61

1.36


TMEM106B

4.98E-04

1.77E-05

2.12E-14

8.24E-04

-1.51

-1.70


C9orf142

5.85E-12

4.64E-03

4.62E-05

8.46E-04

1.90

-1.21


ADRM1

2.00E-05

9.59E-01

1.31E-04

8.49E-04

1.40

1.00


NOC4L

6.75E-04

3.10E-04

2.61E-03

8.54E-04

1.46

1.50


ZFYVE16

6.13E-04

1.66E-02

1.16E-03

8.63E-04

-1.54

-1.33


HPS1

1.80E-04

5.28E-04

1.53E-03

8.68E-04

1.72

1.64


RAB4B

2.82E-05

6.19E-06

1.50E-04

8.90E-04

2.82

3.14


MUT

2.14E-05

2.01E-06

7.54E-05

8.96E-04

-1.66

1.79


HNRNPL

4.63E-06

5.51E-03

1.18E-01

9.18E-04

1.61

1.30


LIN7C

2.12E-04

1.28E-06

5.96E-07

9.22E-04

-1.61

-1.96


VCPIP1

1.49E-03

3.15E-06

5.03E-02

9.42E-04

-1.42

-1.76


DLD

9.70E-04

8.80E-08

1.75E-03

9.49E-04

-1.49

-2.09


DLAT

2.09E-05

3.75E-02

1.21E-06

9.73E-04

-1.54

-1.21


FGF13

2.54E-04

6.38E-08

8.76E-03

9.89E-04

-1.75

-2.55


C5orf41

7.05E-05

1.75E-09

5.73E-03

1.05E-03

-1.48

-2.01


TMEM134

2.70E-08

5.91E-02

1.18E-03

1.05E-03

2.00

-1.21


C12orf39

4.41E-12

3.12E-03

2.44E-05

1.06E-03

-6.13

1.75


YAP1

2.16E-06

5.80E-07

1.46E-04

1.08E-03

-1.58

-1.64


NOC2L

2.15E-04

2.66E-02

6.49E-04

1.10E-03

1.63

-1.32


MAL2

3.09E-04

8.75E-06

2.33E-02

1.12E-03

1.87

-2.25


PTPLAD1

1.17E-05

8.28E-10

2.11E-02

1.13E-03

1.43

-1.78


SDC3

1.95E-03

1.05E-01

9.52E-02

1.14E-03

1.48

1.21


CCNL2

2.72E-04

6.33E-01

1.73E-02

1.15E-03

1.60

1.06


ARHGEF15

8.73E-06

8.29E-01

4.72E-02

1.18E-03

-2.02

1.03


IFIT5

7.61E-04

7.57E-12

1.27E-02

1.18E-03

-1.45

-2.76


PDGFC

1.44E-05

1.94E-08

1.92E-06

1.19E-03

-1.74

-2.22


HIP1R

5.96E-04

7.12E-06

2.55E-02

1.19E-03

1.50

1.76


FBXL18

4.98E-04

1.16E-02

9.70E-02

1.20E-03

1.68

1.44


PDLIM7

4.33E-05

1.22E-04

1.34E-02

1.22E-03

1.70

1.63


LOC90379

2.62E-04

2.22E-04

1.45E-03

1.23E-03

1.73

1.74


CLDN5

2.33E-03

1.21E-03

4.47E-01

1.24E-03

-1.90

-2.00


ZNF558

6.51E-04

3.18E-06

2.49E-06

1.25E-03

-1.41

-1.67


ATP8A1

9.49E-04

3.31E-03

1.32E-03

1.29E-03

1.86

1.72


HTF9C

8.06E-05

7.73E-03

3.66E-03

1.30E-03

1.62

1.36


TOP1MT

1.04E-05

7.89E-04

1.88E-04

1.30E-03

1.59

1.39


DDIT3

3.71E-05

3.25E-01

1.58E-02

1.31E-03

1.64

1.11


HSF1

7.00E-05

4.86E-03

1.29E-02

1.32E-03

2.53

1.86


APRT

5.71E-08

3.55E-01

1.22E-04

1.33E-03

2.36

-1.12


C17orf49

1.48E-06

2.40E-03

8.03E-04

1.35E-03

1.45

-1.23


GABARAPL2

7.79E-05

1.43E-08

3.81E-05

1.36E-03

-1.53

-2.00


PRKAA1

6.97E-07

5.50E-01

4.02E-03

1.37E-03

-1.53

-1.04


PLXNA4B

2.90E-06

1.93E-05

1.03E-02

1.40E-03

-3.29

2.87


SPPL2B

1.84E-04

9.70E-01

8.27E-03

1.46E-03

1.65

-1.00


IL17RC

4.01E-04

2.18E-01

2.42E-04

1.46E-03

1.73

1.19


C9orf66

5.23E-04

3.12E-03

1.62E-01

1.47E-03

-1.56

-1.45


PPAT

3.48E-05

4.79E-01

5.33E-02

1.47E-03

1.55

1.07


ENO3

2.55E-06

7.64E-03

5.28E-04

1.47E-03

1.94

-1.40


NUP85

1.61E-07

5.16E-03

1.79E-01

1.48E-03

1.65

-1.26


JMJD1B

5.67E-05

2.06E-08

2.51E-06

1.49E-03

-1.64

-2.19


C20orf149

4.13E-08

4.50E-03

3.19E-02

1.49E-03

1.89

1.32


LRRTM2

7.98E-09

4.21E-04

1.94E-06

1.50E-03

-2.43

-1.58


NSUN5

1.64E-06

2.55E-02

6.91E-03

1.52E-03

1.44

1.16


C15orf48

1.08E-04

3.77E-07

2.00E-04

1.52E-03

1.77

-2.25


SHROOM2

5.44E-05

2.24E-02

6.12E-01

1.52E-03

2.38

-1.57


TMCC1

8.49E-04

1.92E-01

1.62E-03

1.53E-03

1.42

1.14


TMEM16C

1.82E-05

4.87E-05

5.35E-02

1.54E-03

-1.99

-1.90


MRPL53

3.95E-04

1.70E-01

2.16E-03

1.54E-03

1.42

-1.13


IGSF3

1.45E-03

3.95E-08

7.32E-03

1.61E-03

1.73

-3.02


ALG1

1.09E-07

4.88E-04

3.86E-02

1.61E-03

2.42

1.67


ICOSLG

8.82E-04

6.33E-04

1.25E-02

1.72E-03

1.57

1.59


PHC2

1.51E-04

1.36E-01

6.48E-02

1.72E-03

1.66

1.20


UBFD1

2.24E-08

3.23E-01

8.08E-02

1.78E-03

1.99

1.10


RPS3

5.32E-06

1.85E-02

8.89E-03

1.88E-03

1.53

1.22


CTF8

1.51E-05

1.01E-08

1.58E-02

1.90E-03

1.83

2.44


TCOF1

1.06E-03

1.69E-04

6.12E-05

1.90E-03

1.47

1.58


LOC407835

1.67E-05

4.40E-03

1.22E-03

1.91E-03

1.80

1.43


MIB2

1.02E-03

7.29E-03

1.51E-02

1.91E-03

1.45

1.34


SPATA13

2.19E-03

1.67E-08

4.23E-01

1.95E-03

1.44

2.22


C11orf73

6.88E-04

2.78E-15

1.69E-02

1.97E-03

-1.51

-4.38


PPAN

6.63E-04

5.04E-01

3.06E-03

1.98E-03

1.56

1.08


LACTB2

1.98E-06

4.55E-01

5.63E-06

1.98E-03

-2.06

1.10


FVT1

5.84E-06

5.82E-04

2.24E-07

1.99E-03

-1.77

-1.50


NRARP

1.04E-03

1.58E-04

7.55E-05

2.01E-03

2.14

2.47


C10orf97

1.31E-07

1.14E-01

3.59E-08

2.09E-03

-1.82

1.16


Kibriya et al. BMC Genomics 2010 11:622   doi:10.1186/1471-2164-11-622

Open Data