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Table 6 Differentially expressed genes common to 2 or more LIMMA comparisons between: 9 prototypical SCPC, 9 prototypical AdCa, and 4 atypical SCPC, with associated centroids

From: Gene expression signatures of neuroendocrine prostate cancer and primary small cell prostatic carcinoma

Gene AD SC AS AD (SCAN) SC (SCAN) AS (SCAN)
TPX2 5.40 6.73 7.41 0.16 1.10 1.33
CHEK1 4.42 5.54 6.12 0.02 0.46 0.55
CKAP2L 4.67 5.57 5.70 -0.04 0.41 0.29
HMMR 3.99 4.76 5.17 -0.07 0.25 0.30
CDCA2 4.32 5.05 5.45 -0.13 0.19 0.29
KIF15 4.16 5.15 5.26 -0.07 0.41 0.39
ARHGAP11B 5.11 5.94 6.23 0.05 0.44 0.51
ANLN 4.60 5.57 6.10 0.00 0.49 0.61
WDHD1 4.35 5.07 5.75 0.02 0.31 0.47
NCAPG2 4.60 5.37 5.73 0.03 0.39 0.48
TMPO 5.88 6.74 7.37 0.30 0.97 1.21
KIF2C 4.60 5.21 5.29 -0.11 0.14 0.15
CASC5 4.35 5.18 5.44 -0.04 0.43 0.44
DLGAP5 4.21 5.49 5.96 -0.04 0.68 0.73
TIMELESS 5.28 5.65 6.04 -0.06 0.14 0.28
HMGB2 7.22 8.47 9.12 0.29 0.84 0.94
IQGAP3 5.49 6.18 6.25 -0.04 0.38 0.35
MKI67 5.15 6.51 6.97 0.01 0.90 0.96
STMN1 5.94 7.12 7.23 0.11 0.92 0.91
PBK 3.80 4.85 5.34 -0.12 0.28 0.34
SKA3 4.30 5.49 5.85 -0.02 0.56 0.63
ARHGAP11A 4.51 5.49 5.87 -0.10 0.37 0.36
TOP2A 5.21 6.94 7.84 0.16 1.37 1.66
E2F7 5.17 5.91 6.05 -0.08 0.33 0.30
HJURP 5.65 6.67 6.77 0.00 0.54 0.55
CDC7 4.15 4.97 5.27 -0.07 0.27 0.34
BRIP1 4.03 4.92 5.46 -0.08 0.36 0.52
KIF11 3.94 4.95 5.49 -0.09 0.49 0.58
UBE2C 6.45 7.38 7.59 0.12 0.96 1.12
PTTG1 7.10 9.16 9.20 0.23 1.25 1.08
NCAPG 4.46 5.81 6.25 0.11 0.90 0.95
HIST1H2AJ 7.10 8.15 8.55 0.32 0.99 1.27
CENPF 4.86 6.51 6.96 -0.02 0.90 1.00
ASPM 4.27 5.74 6.28 -0.06 0.71 0.83
CIT 5.29 6.02 6.17 -0.06 0.38 0.38
NEK2 4.90 5.63 5.98 -0.06 0.24 0.33
CDKN2C 5.32 6.21 6.37 -0.19 0.19 0.25
HIST1H2BO 6.51 8.04 7.88 -0.08 1.06 1.32
MELK 4.20 5.26 5.54 -0.04 0.58 0.53
NDC80 4.20 5.54 5.82 -0.02 0.65 0.63
HIST1H4C 7.86 9.06 9.35 1.25 2.35 2.26
CENPK 4.11 5.32 5.94 -0.01 0.47 0.57
GINS1 4.49 5.59 6.22 -0.11 0.43 0.66
CDKN3 4.81 6.06 6.81 -0.03 0.49 0.59
CNIH2 6.08 6.60 6.84 0.04 0.28 0.33
ESCO2 4.06 4.55 4.69 -0.17 0.00 0.05
NUF2 4.54 5.79 5.66 -0.01 0.57 0.35
NUSAP1 5.47 6.91 7.45 0.15 1.15 1.25
KIF23 4.74 5.64 5.85 -0.01 0.46 0.38
CDK1 4.10 5.08 5.22 -0.04 0.40 0.41
FBXO5 5.15 6.19 6.63 0.09 0.56 0.63
CDC20 5.95 6.55 6.71 0.07 0.39 0.45
PLK4 3.94 4.78 5.03 -0.03 0.40 0.39
HIST1H3B 4.87 6.59 7.29 0.19 1.44 1.71
CCNB1 4.96 6.11 6.57 0.05 0.70 0.80
SGOL1 3.99 4.95 5.07 -0.01 0.59 0.54
CENPE 3.83 4.78 5.17 -0.09 0.36 0.42
DEPDC1B 4.43 5.51 5.59 -0.11 0.33 0.27
CLSPN 4.54 5.82 5.69 -0.10 0.53 0.40
CENPW 4.30 5.64 6.14 -0.09 0.50 0.72
FANCI 4.42 5.30 5.67 -0.01 0.46 0.48
LIN9 4.25 4.86 5.26 -0.09 0.14 0.22
DNMT1 6.61 7.25 7.39 0.31 0.71 0.72
KIF4B 5.74 6.30 6.38 0.04 0.48 0.72
ESPL1 5.26 5.77 5.90 -0.14 0.10 0.17
EZH2 5.48 6.38 6.61 0.14 0.68 0.68
LMNB1 5.34 6.66 6.91 0.04 0.63 0.67
CEP55 4.50 5.39 5.40 -0.15 0.25 0.18
WDR76 4.79 6.06 6.25 0.06 0.69 0.69
TUBB2B 7.07 8.17 7.90 -0.08 1.18 0.78
DTL 4.53 5.71 6.23 -0.05 0.56 0.69
KIF18A 3.62 4.73 4.73 -0.16 0.33 0.24
GTSE1 5.29 5.87 5.93 -0.02 0.31 0.31
TROAP 6.58 7.07 7.26 0.12 0.51 0.64
BUB1 4.78 5.78 5.79 -0.06 0.47 0.40
RN7SL720P 3.47 4.19 4.56 -0.35 -0.14 -0.04
SPAG5 5.40 6.11 6.53 0.01 0.39 0.47
MYLK-AS1 6.94 6.22 6.00 0.77 0.41 0.37
CCND1 8.13 7.08 7.32 0.89 0.23 0.44
KLK3 9.85 6.40 9.58 2.87 0.22 2.21
KLK2 9.81 6.22 9.51 2.56 0.12 2.13
ZNF615 6.56 4.71 6.84 0.89 0.06 0.96
TMPRSS2 8.25 5.02 8.01 1.74 -0.01 1.36
NKX3-1 8.29 6.44 8.41 1.19 -0.24 1.25
PMEPA1 7.94 6.31 7.89 1.49 0.29 1.28
HOXB13 8.50 5.43 8.52 1.34 0.08 1.17
KLK4 8.85 6.55 8.85 1.92 0.15 1.70
SNORA59A 5.84 4.94 7.22 0.92 0.35 1.23
ACPP 8.58 4.79 8.04 2.35 0.04 1.59
FOLH1 7.34 4.66 7.25 1.80 0.06 1.37
TRGC1 9.10 4.73 9.17 1.34 -0.02 1.02
ZNF350 6.80 4.77 6.51 0.94 0.11 0.74
BMPR1B 6.51 4.79 7.32 0.99 -0.01 1.28
DSC2 6.29 4.94 6.98 0.57 0.02 0.93
PDE3B 6.41 5.10 6.27 0.60 0.08 0.58
FOLH1B 7.23 4.52 7.07 1.42 -0.05 0.97
ZNF613 7.51 5.95 7.51 1.09 0.44 1.02
RNF138P1 7.21 3.64 7.50 1.71 0.19 1.76
GCNT2 5.33 4.64 5.97 0.22 -0.02 0.44
SLC45A3 8.18 6.42 8.02 1.44 0.04 1.10
PRR16 6.75 5.41 7.02 0.72 0.10 0.81
ZNF614 5.88 4.77 6.04 0.33 0.01 0.47
TULP3 6.15 5.68 6.64 0.67 0.54 0.91
MID2 6.22 5.14 6.20 0.53 0.05 0.51
ZG16B 8.30 7.01 8.42 0.72 0.23 0.72
TRGC2 7.46 4.36 7.37 1.52 -0.03 1.27
ERGIC1 8.17 6.53 8.02 1.37 0.45 1.21
NCOR1 7.25 6.36 7.50 0.92 0.52 1.03
SPDEF 7.90 6.44 7.50 0.96 -0.02 0.66
ALG13 5.81 5.02 6.09 0.66 0.30 0.76
POTEF 7.68 5.37 8.41 1.43 0.36 1.32
GRHL2 7.38 5.24 7.13 1.14 0.14 0.96
SH3RF1 7.21 6.09 7.56 0.93 0.22 1.08
CREB3L4 7.20 5.96 7.23 0.94 0.20 0.90
CAMKK2 7.28 6.14 7.35 0.77 0.20 0.85
WNK1 7.56 6.79 7.91 1.12 0.77 1.38
ZNF649 8.19 6.41 7.90 1.37 0.48 1.19
PPAP2A 7.68 5.97 8.46 1.54 0.43 1.85
C1orf116 7.44 5.93 7.40 1.03 0.20 1.01
ABCC4 7.86 5.32 6.61 1.61 0.07 0.66
ARHGAP6 6.48 5.43 6.79 0.50 -0.11 0.55
RAB27B 5.92 4.77 6.09 0.65 0.09 0.65
ZNF432 6.24 5.02 6.49 0.68 0.18 0.72
ENOSF1 6.27 5.51 6.90 0.48 0.19 0.75
AMELX 5.64 4.66 6.33 0.49 -0.09 0.65
SLC30A4 7.90 5.40 7.18 1.54 0.09 0.91
THRB 5.94 5.27 6.10 0.33 0.04 0.40
HEATR5B 5.58 4.92 5.68 0.48 0.22 0.52
CROT 5.11 4.44 5.11 0.31 0.02 0.23
SLC44A4 8.12 6.08 7.98 1.24 0.14 1.16
TTC19 6.74 6.02 7.26 0.79 0.43 0.87
AADAT 5.86 4.61 6.39 0.62 0.13 0.85
ZNF616 5.48 4.65 5.71 0.37 0.16 0.49
CCDC160 4.51 2.93 4.73 0.26 -0.10 0.27
STEAP2 8.17 5.62 7.86 2.06 0.25 1.58
ADPRM 5.11 4.37 5.25 0.28 -0.01 0.33
TBX3 7.10 6.03 7.56 0.63 -0.04 0.90
AR 7.65 6.02 7.84 1.05 0.16 1.15
EEF2 9.77 8.60 9.66 2.47 1.48 2.22
ZNF880 6.65 5.81 6.93 0.55 0.22 0.76
HERC3 6.69 5.54 6.71 0.97 0.32 0.87
NEDD4L 7.45 5.39 7.06 1.11 0.20 0.78
ARSD-AS1 6.76 5.14 6.72 1.69 0.38 1.60
ZNF33A 5.91 5.06 6.29 0.55 0.33 0.71
MIOS 6.13 4.91 6.48 0.74 0.28 0.84
CPNE4 7.81 4.49 6.25 1.66 0.00 0.72
ARSD 6.71 5.61 6.72 0.14 -0.20 0.14
IQGAP2 5.76 4.62 5.57 0.53 0.03 0.38
ACACA 7.16 5.69 7.38 1.08 0.34 1.15
MALT1 6.63 4.97 6.44 1.11 0.15 0.86
KIAA1551 6.74 5.97 7.04 1.02 0.73 1.35
KIAA1244 7.94 6.21 7.93 1.31 0.31 1.26
REPS2 7.03 5.62 7.20 0.75 0.05 0.71
RASSF3 6.16 5.16 6.40 0.75 0.20 0.88
ADIPOR2 6.74 6.21 7.09 0.53 0.33 0.73
CLK4 6.11 4.96 6.33 0.62 0.25 0.69
AMD1 7.13 5.86 7.68 1.24 0.48 1.45
SLC35F2 5.68 4.57 5.47 0.05 -0.24 -0.04
SCMH1 7.15 6.38 7.33 0.93 0.52 1.00
ALDH6A1 6.38 5.63 6.33 0.58 0.16 0.51
PDE9A 7.15 5.59 6.73 0.73 0.02 0.54
KDM5A 5.97 5.32 6.41 0.44 0.27 0.67
ANKRD50 6.73 5.65 7.62 0.90 0.50 1.52
C1orf21 7.85 6.74 8.10 1.02 0.45 1.16
GNB2L1 10.03 8.98 10.40 1.33 1.00 1.49
RANBP3L 5.85 4.26 6.10 0.71 0.00 0.76
IGBP1 6.68 6.16 6.97 0.63 0.40 0.79
PPAPDC1B 7.17 6.12 7.02 0.78 0.11 0.63
MSMB 8.43 4.45 8.34 2.39 0.03 1.94
C12orf4 5.08 4.50 5.45 0.33 0.09 0.50
ZNF577 7.30 5.57 6.78 1.16 0.28 0.90
ZNF841 6.67 5.55 6.69 1.15 0.51 1.11
RN7SL97P 3.75 4.77 3.57 -0.45 -0.16 -0.54
POTEH 8.09 4.74 9.36    
POTEH-AS1 7.54 5.60 7.79    
FAM115A 6.88 6.04 6.98    
  1. Legend: Cohorts of 9 prototypical adenocarcinomas, 9 prototypical SCPCs, and 4 atypical SCPCs were formed from meta-9 clusters after removing outliers, mixed adenocarcinomas, adenocarcinomas associated with NE differentiation, and samples archived over 10 years in FFPE. Differentially expressed genes were calculated by LIMMA for all possible pair-wise comparisons of cohorts, and filtered for genes shared by 2 or more comparisons. This resulted in 176 genes consisting of 79 genes (77 up, 2 down) differentially expressed in common between either prototypical SCPCs or atypical SCPCs versus prototypical adenocarcinomas, and 97 genes (1 up, 96 down) differentially expressed in common between prototypical SCPCs and either prototypical adenocarcinomas or atypical SCPCs. Centroids for each cohort (values in the table) were formed for this gene-set and transferred to the GRID database under SCAN normalization for use in a nearest-centroid classifier model