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 |