Background
Methods
Tissue and patient characteristics
Number and sex of patients |
n = 24 (females n = 7, males n = 17) | |
---|---|---|
Ethnicity | Caucasian n = 21 Asian n = 3 | |
Age at surgery | Total: 68.4 years (±12.3) | |
Females: 65.4 years (±21.5) | ||
Males: 69.5 years (±8.5) | ||
Postoperative survival (deceased individuals) | 13.3 months (±8.8) | |
Postoperative survival (alive individuals at study end) | 46.0 months (±8.0) | |
Tumor size | 47 mm (±28) | |
Tumor stage | T1 | 3 |
T2 | 13 | |
T3 | 5 | |
T4 | 3 | |
Nodal stage | N0 | 11 |
N1 | 8 | |
N2 | 3 | |
N3 | 2 | |
Histological type | Intestinal | 6 |
Diffuse | 14 | |
Mixed | 4 |
Methylation assays
Immunohistochemistry
Statistical analysis
Results
General description
Rank product testing
Filtering of statistical CpG sites
Clinicopathological correlation
Post-op survival | Lymph node metastasis | Tumor size | Lauren classification | Metaplasia | Atrophy |
H. pylori
| |
---|---|---|---|---|---|---|---|
CpgID/Gene promoter Hypermethylated in the tumor | |||||||
cg09350274/GFRA3 |
r = −0.69 p = 0.002 |
r = 0.52 p = 0.028 |
r = 0.48 p = 0.42 |
r = 0.480 p = 0.044 |
r = −0.590 p = 0.01 | ||
cg02720618/ESR1 |
r = 0.56 p = 0.016 | ||||||
cg04623837/HCG9 |
r = 0.64 p = 0.004 | ||||||
cg07307078/TUBB6 |
r = 0.49 p = 0.04 | ||||||
cg08615333/TGFB3 |
r = 0.5 p = 0.037 |
r = 0.504 p = 0.033 | |||||
cg01566170/CAPN2 |
r = −0.53 p = 0.023 |
r = 0.526 p = 0.025 | |||||
cg16986846/SCGB2A1 |
r = −0.576 p = 0.012 | ||||||
cg02633817/FXYD3 |
r = −0.474 p = 0.047 | ||||||
cg20640433/LAMA2 |
r = 524 p = 0.026 | ||||||
cg21905630/GSH2 |
r = 0.52 p = 0.028 | ||||||
cg13718960/RNASE1 |
r = 0.554 p = 0.017 | ||||||
cg19118812/ELMO1 |
r = −0.546 p = 0.019 | ||||||
cg26557658/FAM43B |
r = −0.604 p = 0.008 | ||||||
cg03616357/FLJ21159 |
r = 0.574 p = 0.013 | ||||||
cg08615333/TGFB3 |
r = 0.504 p = 0.033 | ||||||
cg14189571/ZFP42 |
r = 0.484 p = 0.042 | ||||||
cg17872757/FLI1 |
r = 0.495 p = 0.037 | ||||||
cg21790626/ZNF154 |
r = 0.573 p = 0.013 | ||||||
cg27546237/COL4A1 |
r = 0.527 p = 0.025 | ||||||
CpgID/Gene promoter Hypomethylated in the tumor | |||||||
cg13694749/SCN4A |
r = −0.638 p = 0.004 | ||||||
cg18059088/HS3ST1 |
r = −0.474 p = 0.047 | ||||||
cg26619317/CNN3 |
r = 0.481 p = 0.043 | ||||||
cg07131544/NCR2 |
r = 0.496 p = 0.036 | ||||||
cg14696870/FCER1A |
r = −0.567 p = 0.014 | ||||||
cg20676475/LCE3D |
r = −0.708 p = 0.001 | ||||||
cg00974864/FCGR3B |
r = −562 p = 0.015 | ||||||
cg13180098/RHO |
r = −0.604 p = 0.008 |
r = −0.597 p = 0.009 |
r = 0.682 p = 0.002 | ||||
cg24691453/S100A4 |
r = 0.470 p = 0.49 | ||||||
cg15309006/LOC63928 |
r = −0.499 p = 0.035 | ||||||
cg26789453/TMEM116 |
r = −0.512 p = 0.030 | ||||||
cg26264314/NALP5 |
r = −0.474 p = 0.047 | ||||||
cg20383064/BFSP2 |
r = −0.487 p = 0.040 | ||||||
cg25119415/MNDA |
r = −0.646 p = 0.004 |
r = −0.514 p = 0.029 |
r = 0.547 p = 0.019 | ||||
cg14603345/BTBD3 |
p = −0.483 r = 0.042 | ||||||
cg17356733/IFNGR2 |
r = −0.480 p = 0.044 | ||||||
cg23756272/BCL2 |
r = −0.500 p = 0.035 | ||||||
cg00842351/TJP2 |
r = −527 p = 0.24 | ||||||
cg25248094/SH2D1A |
r = 0.487 p = 0.041 |
r = −0.526 p = 0.025 | |||||
cg04454050/TREML1 | 0.474 0.047 | ||||||
cg02611419/KCNK17 |
r = −502 p = 0.034 | ||||||
cg05252264/FCAR |
r = 0.587 p = 0.10 | ||||||
cg22268164/TRHR |
r = −0.619 p = 0.006 | ||||||
cg02046017/LOC220070 |
r = 0.475 p = 0.046 | ||||||
cg09191232/PAPSS1 |
r = −0.581 p = 0.011 |
Gene expression correlation
Gene promoter/gene | Pearson coefficient |
P value | Spearman’s rho |
P-value |
---|---|---|---|---|
CPD | NS | −0.482 | 0.043 | |
DEFB106A | −0.531 | 0.23 | −0.529 | 0.024 |
FCGR3B | −0.575 | 0.13 | −0.569 | 0.014 |
GATA4 | NS | −0.643 | 0.004 |
Gene promoter/gene | Pearson coefficient |
P value | Spearman’s rho |
P-value |
---|---|---|---|---|
DHX32 | −0.495 | 0.037 | −0.624 | 0.006 |
PPYR | NS | −0.490 | 0.039 | |
FOXI1 | −0.683 | 0.002 | −0.511 | 0.03 |
ORM1 | −0.594 | 0.009 | −0.670 | 0.002 |
ZSCAN18 | Ns | −0.511 | 0.030 | |
PXDN | −0.480 | 0.44 | −0.579 | 0.012 |
Gene promoter/gene | Pearson coefficient |
P value | Spearman’s rho |
P-value |
---|---|---|---|---|
SPP1 | ns | −0.523 | 0.026 | |
ALDH3A1 | ns | −0.560 | 0.016 | |
TCN1 | ns | −0.521 | 0.027 |
Pathway name | Impact factor |
p-value |
---|---|---|
Natural killer cell mediated cytotoxicity | 6.7 | 0.008 |
Hematopoietic cell lineage | 5.1 | 0.017 |
Colorectal cancer | 5.0 | 0.018 |
Cytokine-cytokine receptor interaction | 5.4 | 0.022 |
Bladder cancer | 4.8 | 0.029 |
Endometrial cancer | 4.9 | 0.046 |