This pipeline uses various statistical tests to identify genes whose promoter methylation levels correlated to selected clinical features.
Testing the association between 16616 genes and 3 clinical features across 173 samples, statistically thresholded by Q value < 0.05, 3 clinical features related to at least one genes.
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2 genes correlated to 'Time to Death'.
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AGRN , C10ORF128
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36 genes correlated to 'AGE'.
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KIAA1377 , JAKMIP1 , TRIM58 , AASS , TMEM20 , ...
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11 genes correlated to 'GENDER'.
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FAM35A , DKFZP434L187 , KIF4B , CROCC , WBP11P1 , ...
Complete statistical result table is provided in Supplement Table 1
Clinical feature | Statistical test | Significant genes | Associated with | Associated with | ||
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Time to Death | Cox regression test | N=2 | shorter survival | N=1 | longer survival | N=1 |
AGE | Spearman correlation test | N=36 | older | N=7 | younger | N=29 |
GENDER | t test | N=11 | male | N=7 | female | N=4 |
Time to Death | Duration (Months) | 0.9-94.1 (median=12.5) |
censored | N = 59 | |
death | N = 91 | |
Significant markers | N = 2 | |
associated with shorter survival | 1 | |
associated with longer survival | 1 |
HazardRatio | Wald_P | Q | C_index | |
---|---|---|---|---|
AGRN | 290000001 | 1.03e-09 | 1.7e-05 | 0.541 |
C10ORF128 | 0.12 | 5.767e-07 | 0.0096 | 0.369 |
AGE | Mean (SD) | 55.17 (16) |
Significant markers | N = 36 | |
pos. correlated | 7 | |
neg. correlated | 29 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
KIAA1377 | -0.4586 | 2.217e-10 | 3.68e-06 |
JAKMIP1 | -0.4558 | 2.933e-10 | 4.87e-06 |
TRIM58 | 0.413 | 1.629e-08 | 0.000271 |
AASS | -0.4022 | 4.115e-08 | 0.000684 |
TMEM20 | -0.4015 | 4.388e-08 | 0.000729 |
HIST3H2A | -0.389 | 1.226e-07 | 0.00204 |
C21ORF70 | -0.3863 | 1.521e-07 | 0.00253 |
TBC1D12 | -0.385 | 1.69e-07 | 0.00281 |
CD96 | 0.3831 | 1.975e-07 | 0.00328 |
APBB1 | -0.38 | 2.506e-07 | 0.00416 |
GENDER | Labels | N |
FEMALE | 83 | |
MALE | 90 | |
Significant markers | N = 11 | |
Higher in MALE | 7 | |
Higher in FEMALE | 4 |
T(pos if higher in 'MALE') | ttestP | Q | AUC | |
---|---|---|---|---|
FAM35A | -13.06 | 3.153e-27 | 5.24e-23 | 0.9024 |
DKFZP434L187 | 11.48 | 1.62e-22 | 2.69e-18 | 0.9376 |
KIF4B | -11.58 | 1.665e-22 | 2.77e-18 | 0.8656 |
CROCC | -10 | 9.068e-19 | 1.51e-14 | 0.8842 |
WBP11P1 | 8.51 | 8.854e-15 | 1.47e-10 | 0.8361 |
NARS | -5.73 | 4.522e-08 | 0.000751 | 0.7803 |
FAM186A | 5.37 | 2.982e-07 | 0.00495 | 0.7146 |
POLL | 5.27 | 4.254e-07 | 0.00707 | 0.7129 |
LOC389791 | 5.26 | 4.373e-07 | 0.00726 | 0.7087 |
PLLP | 5.15 | 8.639e-07 | 0.0143 | 0.7331 |
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Expresson data file = LAML.meth.for_correlation.filtered_data.txt
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Clinical data file = LAML.clin.merged.picked.txt
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Number of patients = 173
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Number of genes = 16616
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Number of clinical features = 3
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 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.