This pipeline uses various statistical tests to identify genes whose promoter methylation levels correlated to selected clinical features.
Testing the association between 12742 genes and 7 clinical features across 549 samples, statistically thresholded by Q value < 0.05, 5 clinical features related to at least one genes.
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144 genes correlated to 'AGE'.
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LPA , GRIK2 , FLJ44881 , PCDHGB7 , CNTD1 , ...
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4 genes correlated to 'PRIMARY.SITE.OF.DISEASE'.
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PRH1 , BMPR1B , TAS2R50 , DBN1
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1 gene correlated to 'KARNOFSKY.PERFORMANCE.SCORE'.
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OLFML1
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2144 genes correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
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NID2 , CHRNA9 , MLL3 , FXR2 , EXOC5 , ...
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19 genes correlated to 'NEOADJUVANT.THERAPY'.
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NF1 , TM7SF3 , CCR4 , CDCA2 , CASP3 , ...
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No genes correlated to 'Time to Death', and 'TUMOR.STAGE'.
Complete statistical result table is provided in Supplement Table 1
Clinical feature | Statistical test | Significant genes | Associated with | Associated with | ||
---|---|---|---|---|---|---|
Time to Death | Cox regression test | N=0 | ||||
AGE | Spearman correlation test | N=144 | older | N=18 | younger | N=126 |
PRIMARY SITE OF DISEASE | ANOVA test | N=4 | ||||
KARNOFSKY PERFORMANCE SCORE | Spearman correlation test | N=1 | higher score | N=1 | lower score | N=0 |
TUMOR STAGE | Spearman correlation test | N=0 | ||||
RADIATIONS RADIATION REGIMENINDICATION | t test | N=2144 | yes | N=2096 | no | N=48 |
NEOADJUVANT THERAPY | t test | N=19 | yes | N=7 | no | N=12 |
Time to Death | Duration (Months) | 0.3-180.2 (median=29) |
censored | N = 253 | |
death | N = 290 | |
Significant markers | N = 0 |
AGE | Mean (SD) | 59.73 (12) |
Significant markers | N = 144 | |
pos. correlated | 18 | |
neg. correlated | 126 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
LPA | 0.3052 | 4.421e-13 | 5.63e-09 |
GRIK2 | 0.2992 | 1.308e-12 | 1.67e-08 |
FLJ44881 | -0.2933 | 5.384e-12 | 6.86e-08 |
PCDHGB7 | 0.2849 | 1.604e-11 | 2.04e-07 |
CNTD1 | -0.27 | 1.853e-10 | 2.36e-06 |
INHBE | -0.2667 | 3.131e-10 | 3.99e-06 |
TTLL7 | -0.2626 | 5.995e-10 | 7.64e-06 |
SDR16C5 | -0.261 | 7.639e-10 | 9.73e-06 |
PRLH | -0.2602 | 8.662e-10 | 1.1e-05 |
GPR12 | -0.2554 | 2.297e-09 | 2.92e-05 |
PRIMARY.SITE.OF.DISEASE | Labels | N |
OMENTUM | 2 | |
OVARY | 545 | |
PERITONEUM (OVARY) | 2 | |
Significant markers | N = 4 |
ANOVA_P | Q | |
---|---|---|
PRH1 | 8.359e-10 | 1.07e-05 |
BMPR1B | 2.951e-08 | 0.000376 |
TAS2R50 | 8.842e-07 | 0.0113 |
DBN1 | 1.046e-06 | 0.0133 |
One gene related to 'KARNOFSKY.PERFORMANCE.SCORE'.
KARNOFSKY.PERFORMANCE.SCORE | Mean (SD) | 75.64 (13) |
Score | N | |
40 | 2 | |
60 | 20 | |
80 | 49 | |
100 | 7 | |
Significant markers | N = 1 | |
pos. correlated | 1 | |
neg. correlated | 0 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
OLFML1 | 0.5794 | 3.38e-08 | 0.000431 |
TUMOR.STAGE | Mean (SD) | 3.05 (0.56) |
N | ||
Stage 1 | 16 | |
Stage 2 | 24 | |
Stage 3 | 421 | |
Stage 4 | 83 | |
Significant markers | N = 0 |
2144 genes related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 3 | |
YES | 546 | |
Significant markers | N = 2144 | |
Higher in YES | 2096 | |
Higher in NO | 48 |
T(pos if higher in 'YES') | ttestP | Q | AUC | |
---|---|---|---|---|
NID2 | 27.3 | 2.31e-100 | 2.94e-96 | 0.9829 |
CHRNA9 | 28.28 | 3.239e-94 | 4.13e-90 | 0.8765 |
MLL3 | 22.58 | 1.441e-73 | 1.84e-69 | 0.8767 |
FXR2 | 21.37 | 6.892e-69 | 8.78e-65 | 0.9609 |
EXOC5 | 21.03 | 8.412e-67 | 1.07e-62 | 0.9104 |
DVL2 | 19.75 | 6.859e-66 | 8.74e-62 | 0.8657 |
RNF130 | 19.16 | 8.573e-63 | 1.09e-58 | 0.8663 |
NPPB | 18.98 | 4.221e-62 | 5.37e-58 | 0.8541 |
FKBP3 | 18.83 | 3.703e-61 | 4.72e-57 | 0.8712 |
CDCA7 | 18.61 | 1.143e-59 | 1.46e-55 | 0.8773 |
NEOADJUVANT.THERAPY | Labels | N |
NO | 441 | |
YES | 108 | |
Significant markers | N = 19 | |
Higher in YES | 7 | |
Higher in NO | 12 |
T(pos if higher in 'YES') | ttestP | Q | AUC | |
---|---|---|---|---|
NF1 | -5.36 | 1.883e-07 | 0.0024 | 0.6315 |
TM7SF3 | -5.25 | 2.783e-07 | 0.00355 | 0.5927 |
CCR4 | 5.14 | 4.881e-07 | 0.00622 | 0.6277 |
CDCA2 | -5.11 | 5.377e-07 | 0.00685 | 0.6028 |
CASP3 | 5.1 | 7.371e-07 | 0.00939 | 0.6306 |
KLRA1 | 5.07 | 8.368e-07 | 0.0107 | 0.6241 |
DZIP3 | -5.01 | 8.808e-07 | 0.0112 | 0.5866 |
ZEB1 | -4.98 | 1.138e-06 | 0.0145 | 0.6002 |
TLL1 | -4.98 | 1.155e-06 | 0.0147 | 0.6037 |
TFCP2L1 | -4.87 | 1.713e-06 | 0.0218 | 0.6147 |
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Expresson data file = OV.meth.for_correlation.filtered_data.txt
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Clinical data file = OV.clin.merged.picked.txt
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Number of patients = 549
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Number of genes = 12742
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Number of clinical features = 7
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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.