Skip to main content

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.

From: Analyses and interpretation of whole-genome gene expression from formalin-fixed paraffin-embedded tissue: an illustration with breast cancer tissues

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