This pipeline uses various statistical tests to identify genes whose promoter methylation levels correlated to selected clinical features.
Testing the association between 19984 genes and 14 clinical features across 417 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 10 clinical features related to at least one genes.
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24 genes correlated to 'AGE'.
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KIAA1143 , KIF15 , BMP8A , NHLRC1 , CLEC5A , ...
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2 genes correlated to 'NEOPLASM.DISEASESTAGE'.
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NOLC1 , ENDOD1
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52 genes correlated to 'PATHOLOGY.T.STAGE'.
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ACBD5 , TACC2 , SLC41A3 , PRDM15 , GLT1D1 , ...
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9 genes correlated to 'PATHOLOGY.N.STAGE'.
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POLR2J3__1 , GPRIN2 , MRPS17 , LZIC , NMNAT1 , ...
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191 genes correlated to 'GENDER'.
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KIF4B , EIF4A1 , SNORA48 , ATP5J , GABPA , ...
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23 genes correlated to 'HISTOLOGICAL.TYPE'.
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LOC150622 , IQGAP1 , TRIM8 , RILP , ZMIZ1 , ...
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5 genes correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
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DNAJC5 , MRPS23 , C18ORF54 , EIF5A , SCYL2__1
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4 genes correlated to 'NUMBERPACKYEARSSMOKED'.
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FAM128A__1 , LOC150776__1 , BHMT2 , DMGDH
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3 genes correlated to 'COMPLETENESS.OF.RESECTION'.
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APBB3 , SLC35A4 , CDC23
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13 genes correlated to 'RACE'.
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GPBAR1 , LOC100133161 , LOC253039 , PSMD5 , CS , ...
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No genes correlated to 'Time to Death', 'PATHOLOGY.M.STAGE', 'KARNOFSKY.PERFORMANCE.SCORE', and 'ETHNICITY'.
Complete statistical result table is provided in Supplement Table 1
Table 1. Get Full Table This table shows the clinical features, statistical methods used, and the number of genes that are significantly associated with each clinical feature at P value < 0.05 and Q value < 0.3.
Clinical feature | Statistical test | Significant genes | Associated with | Associated with | ||
---|---|---|---|---|---|---|
Time to Death | Cox regression test | N=0 | ||||
AGE | Spearman correlation test | N=24 | older | N=13 | younger | N=11 |
NEOPLASM DISEASESTAGE | Kruskal-Wallis test | N=2 | ||||
PATHOLOGY T STAGE | Spearman correlation test | N=52 | higher stage | N=19 | lower stage | N=33 |
PATHOLOGY N STAGE | Spearman correlation test | N=9 | higher stage | N=2 | lower stage | N=7 |
PATHOLOGY M STAGE | Kruskal-Wallis test | N=0 | ||||
GENDER | Wilcoxon test | N=191 | male | N=191 | female | N=0 |
KARNOFSKY PERFORMANCE SCORE | Spearman correlation test | N=0 | ||||
HISTOLOGICAL TYPE | Kruskal-Wallis test | N=23 | ||||
RADIATIONS RADIATION REGIMENINDICATION | Wilcoxon test | N=5 | yes | N=5 | no | N=0 |
NUMBERPACKYEARSSMOKED | Spearman correlation test | N=4 | higher numberpackyearssmoked | N=0 | lower numberpackyearssmoked | N=4 |
COMPLETENESS OF RESECTION | Kruskal-Wallis test | N=3 | ||||
RACE | Kruskal-Wallis test | N=13 | ||||
ETHNICITY | Wilcoxon test | N=0 |
Table S1. Basic characteristics of clinical feature: 'Time to Death'
Time to Death | Duration (Years) | 1-2696 (median=426.5) |
censored | N = 292 | |
death | N = 72 | |
Significant markers | N = 0 |
Table S2. Basic characteristics of clinical feature: 'AGE'
AGE | Mean (SD) | 65.31 (9.9) |
Significant markers | N = 24 | |
pos. correlated | 13 | |
neg. correlated | 11 |
Table S3. Get Full Table List of top 10 genes significantly correlated to 'AGE' by Spearman correlation test
SpearmanCorr | corrP | Q | |
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KIAA1143 | 0.2745 | 3.903e-08 | 0.00078 |
KIF15 | 0.2745 | 3.903e-08 | 0.00078 |
BMP8A | 0.2683 | 8.023e-08 | 0.0016 |
NHLRC1 | 0.2514 | 5.236e-07 | 0.0105 |
CLEC5A | 0.2505 | 5.77e-07 | 0.0115 |
B4GALNT4 | 0.2476 | 7.849e-07 | 0.0157 |
LOC148696 | -0.2416 | 1.465e-06 | 0.0293 |
CYP3A4 | 0.2344 | 3.046e-06 | 0.0609 |
UBE2L6 | -0.2342 | 3.125e-06 | 0.0624 |
ELOVL2 | 0.2337 | 3.268e-06 | 0.0653 |
Table S4. Basic characteristics of clinical feature: 'NEOPLASM.DISEASESTAGE'
NEOPLASM.DISEASESTAGE | Labels | N |
STAGE I | 4 | |
STAGE IA | 101 | |
STAGE IB | 118 | |
STAGE IIA | 46 | |
STAGE IIB | 59 | |
STAGE IIIA | 60 | |
STAGE IIIB | 9 | |
STAGE IV | 19 | |
Significant markers | N = 2 |
Table S5. Get Full Table List of 2 genes differentially expressed by 'NEOPLASM.DISEASESTAGE'
ANOVA_P | Q | |
---|---|---|
NOLC1 | 4.964e-06 | 0.0992 |
ENDOD1 | 1.438e-05 | 0.287 |
Table S6. Basic characteristics of clinical feature: 'PATHOLOGY.T.STAGE'
PATHOLOGY.T.STAGE | Mean (SD) | 1.84 (0.72) |
N | ||
1 | 131 | |
2 | 232 | |
3 | 36 | |
4 | 15 | |
Significant markers | N = 52 | |
pos. correlated | 19 | |
neg. correlated | 33 |
Table S7. Get Full Table List of top 10 genes significantly correlated to 'PATHOLOGY.T.STAGE' by Spearman correlation test
SpearmanCorr | corrP | Q | |
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ACBD5 | -0.2783 | 8.412e-09 | 0.000168 |
TACC2 | -0.2624 | 6.044e-08 | 0.00121 |
SLC41A3 | -0.262 | 6.316e-08 | 0.00126 |
PRDM15 | 0.2536 | 1.686e-07 | 0.00337 |
GLT1D1 | 0.2535 | 1.707e-07 | 0.00341 |
DDX21 | -0.2513 | 2.212e-07 | 0.00442 |
LSS | -0.2464 | 3.833e-07 | 0.00766 |
MCM3APAS | -0.2464 | 3.833e-07 | 0.00766 |
NME1-NME2 | -0.244 | 5.03e-07 | 0.01 |
NME2 | -0.244 | 5.03e-07 | 0.01 |
Table S8. Basic characteristics of clinical feature: 'PATHOLOGY.N.STAGE'
PATHOLOGY.N.STAGE | Mean (SD) | 0.51 (0.76) |
N | ||
0 | 266 | |
1 | 78 | |
2 | 63 | |
3 | 1 | |
Significant markers | N = 9 | |
pos. correlated | 2 | |
neg. correlated | 7 |
Table S9. Get Full Table List of 9 genes significantly correlated to 'PATHOLOGY.N.STAGE' by Spearman correlation test
SpearmanCorr | corrP | Q | |
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POLR2J3__1 | -0.2319 | 2.2e-06 | 0.044 |
GPRIN2 | 0.2311 | 2.38e-06 | 0.0476 |
MRPS17 | -0.228 | 3.261e-06 | 0.0652 |
LZIC | -0.221 | 6.605e-06 | 0.132 |
NMNAT1 | -0.221 | 6.605e-06 | 0.132 |
VAMP1 | 0.2179 | 8.909e-06 | 0.178 |
POP7 | -0.2149 | 1.194e-05 | 0.239 |
CHPF | -0.2141 | 1.287e-05 | 0.257 |
TMEM198 | -0.2141 | 1.287e-05 | 0.257 |
Table S10. Basic characteristics of clinical feature: 'PATHOLOGY.M.STAGE'
PATHOLOGY.M.STAGE | Labels | N |
M0 | 272 | |
M1 | 12 | |
M1A | 1 | |
M1B | 4 | |
MX | 124 | |
Significant markers | N = 0 |
Table S11. Basic characteristics of clinical feature: 'GENDER'
GENDER | Labels | N |
FEMALE | 223 | |
MALE | 194 | |
Significant markers | N = 191 | |
Higher in MALE | 191 | |
Higher in FEMALE | 0 |
Table S12. Get Full Table List of top 10 genes differentially expressed by 'GENDER'. 0 significant gene(s) located in sex chromosomes is(are) filtered out.
W(pos if higher in 'MALE') | wilcoxontestP | Q | AUC | |
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KIF4B | 6656 | 3.171e-34 | 6.34e-30 | 0.8461 |
EIF4A1 | 9340 | 1.351e-23 | 2.7e-19 | 0.7841 |
SNORA48 | 9340 | 1.351e-23 | 2.7e-19 | 0.7841 |
ATP5J | 31554 | 6.321e-16 | 1.26e-11 | 0.7294 |
GABPA | 31554 | 6.321e-16 | 1.26e-11 | 0.7294 |
RWDD2B | 11880 | 1.976e-15 | 3.95e-11 | 0.7254 |
RNASEH2C | 31281 | 3.824e-15 | 7.64e-11 | 0.7231 |
COX7C | 12006 | 4.498e-15 | 8.99e-11 | 0.7225 |
FUBP3 | 12170 | 1.292e-14 | 2.58e-10 | 0.7187 |
LOC100272217 | 12170 | 1.292e-14 | 2.58e-10 | 0.7187 |
No gene related to 'KARNOFSKY.PERFORMANCE.SCORE'.
Table S13. Basic characteristics of clinical feature: 'KARNOFSKY.PERFORMANCE.SCORE'
KARNOFSKY.PERFORMANCE.SCORE | Mean (SD) | 84.21 (22) |
Significant markers | N = 0 |
Table S14. Basic characteristics of clinical feature: 'HISTOLOGICAL.TYPE'
HISTOLOGICAL.TYPE | Labels | N |
LUNG ACINAR ADENOCARCINOMA | 15 | |
LUNG ADENOCARCINOMA MIXED SUBTYPE | 79 | |
LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | 262 | |
LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | 5 | |
LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | 19 | |
LUNG CLEAR CELL ADENOCARCINOMA | 1 | |
LUNG MICROPAPILLARY ADENOCARCINOMA | 3 | |
LUNG MUCINOUS ADENOCARCINOMA | 2 | |
LUNG PAPILLARY ADENOCARCINOMA | 18 | |
LUNG SIGNET RING ADENOCARCINOMA | 1 | |
LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | 5 | |
MUCINOUS (COLLOID) CARCINOMA | 7 | |
Significant markers | N = 23 |
Table S15. Get Full Table List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'
ANOVA_P | Q | |
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LOC150622 | 1.263e-08 | 0.000252 |
IQGAP1 | 1.073e-06 | 0.0214 |
TRIM8 | 2.025e-06 | 0.0405 |
RILP | 2.379e-06 | 0.0475 |
ZMIZ1 | 3.243e-06 | 0.0648 |
FAM46B | 4.792e-06 | 0.0957 |
SHISA4 | 4.803e-06 | 0.096 |
DGKI | 5.144e-06 | 0.103 |
RICH2 | 6.027e-06 | 0.12 |
AVPI1 | 8.242e-06 | 0.165 |
5 genes related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
Table S16. Basic characteristics of clinical feature: 'RADIATIONS.RADIATION.REGIMENINDICATION'
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 18 | |
YES | 399 | |
Significant markers | N = 5 | |
Higher in YES | 5 | |
Higher in NO | 0 |
Table S17. Get Full Table List of 5 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'
W(pos if higher in 'YES') | wilcoxontestP | Q | AUC | |
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DNAJC5 | 1328 | 6.084e-06 | 0.122 | 0.8151 |
MRPS23 | 5849 | 6.378e-06 | 0.127 | 0.8144 |
C18ORF54 | 5824 | 7.041e-06 | 0.141 | 0.813 |
EIF5A | 5790 | 1.105e-05 | 0.221 | 0.8062 |
SCYL2__1 | 5742 | 1.504e-05 | 0.3 | 0.8015 |
Table S18. Basic characteristics of clinical feature: 'NUMBERPACKYEARSSMOKED'
NUMBERPACKYEARSSMOKED | Mean (SD) | 41.14 (27) |
Significant markers | N = 4 | |
pos. correlated | 0 | |
neg. correlated | 4 |
Table S19. Get Full Table List of 4 genes significantly correlated to 'NUMBERPACKYEARSSMOKED' by Spearman correlation test
SpearmanCorr | corrP | Q | |
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FAM128A__1 | -0.2923 | 5.109e-07 | 0.0102 |
LOC150776__1 | -0.2923 | 5.109e-07 | 0.0102 |
BHMT2 | -0.2627 | 6.98e-06 | 0.139 |
DMGDH | -0.2627 | 6.98e-06 | 0.139 |
Table S20. Basic characteristics of clinical feature: 'COMPLETENESS.OF.RESECTION'
COMPLETENESS.OF.RESECTION | Labels | N |
R0 | 276 | |
R1 | 10 | |
R2 | 1 | |
RX | 18 | |
Significant markers | N = 3 |
Table S22. Basic characteristics of clinical feature: 'RACE'
RACE | Labels | N |
ASIAN | 5 | |
BLACK OR AFRICAN AMERICAN | 31 | |
WHITE | 331 | |
Significant markers | N = 13 |
Table S23. Get Full Table List of top 10 genes differentially expressed by 'RACE'
ANOVA_P | Q | |
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GPBAR1 | 7.839e-08 | 0.00157 |
LOC100133161 | 1.858e-07 | 0.00371 |
LOC253039 | 1.865e-07 | 0.00373 |
PSMD5 | 1.865e-07 | 0.00373 |
CS | 3.296e-07 | 0.00659 |
WBSCR27 | 5.301e-07 | 0.0106 |
RGPD5 | 1.181e-06 | 0.0236 |
RGPD8 | 1.181e-06 | 0.0236 |
C14ORF167__1 | 1.377e-06 | 0.0275 |
DHRS4__1 | 1.377e-06 | 0.0275 |
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Expresson data file = LUAD-TP.meth.by_min_clin_corr.data.txt
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Clinical data file = LUAD-TP.merged_data.txt
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Number of patients = 417
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Number of genes = 19984
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Number of clinical features = 14
For survival clinical features, Wald's test in univariate Cox regression analysis with proportional hazards model (Andersen and Gill 1982) was used to estimate the P values using the 'coxph' function in R. Kaplan-Meier survival curves were plot using the four quartile subgroups of patients based on expression levels
For continuous numerical clinical features, Spearman's rank correlation coefficients (Spearman 1904) and two-tailed P values were estimated using 'cor.test' function in R
For multi-class clinical features (ordinal or nominal), one-way analysis of variance (Howell 2002) was applied to compare the log2-expression levels between different clinical classes using 'anova' function in R
For two-class clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the log2-expression levels between the two clinical classes using 't.test' function in R
For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.