This pipeline uses various statistical tests to identify genes whose promoter methylation levels correlated to selected clinical features.
Testing the association between 17322 genes and 3 clinical features across 99 samples, statistically thresholded by Q value < 0.05, 2 clinical features related to at least one genes.
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30 genes correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
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NAA20 , SCD , ZNF280D , HIST1H2BB , ZKSCAN4 , ...
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219 genes correlated to 'NEOADJUVANT.THERAPY'.
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METT10D , DSG3 , KLHL33 , ALDH3A2 , KCTD18 , ...
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No genes correlated to 'AGE'
Complete statistical result table is provided in Supplement Table 1
Clinical feature | Statistical test | Significant genes | Associated with | Associated with | ||
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AGE | Spearman correlation test | N=0 | ||||
RADIATIONS RADIATION REGIMENINDICATION | t test | N=30 | yes | N=21 | no | N=9 |
NEOADJUVANT THERAPY | t test | N=219 | yes | N=130 | no | N=89 |
AGE | Mean (SD) | 61.08 (6.7) |
Significant markers | N = 0 |
30 genes related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 5 | |
YES | 94 | |
Significant markers | N = 30 | |
Higher in YES | 21 | |
Higher in NO | 9 |
T(pos if higher in 'YES') | ttestP | Q | AUC | |
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NAA20 | 9.06 | 7.094e-14 | 1.23e-09 | 0.8681 |
SCD | -8.88 | 2.439e-12 | 4.22e-08 | 0.8511 |
ZNF280D | 7.61 | 9.97e-11 | 1.73e-06 | 0.7638 |
HIST1H2BB | 7.04 | 2.837e-10 | 4.91e-06 | 0.717 |
ZKSCAN4 | 7.95 | 4.126e-10 | 7.15e-06 | 0.8383 |
CLEC4C | -6.74 | 1.439e-09 | 2.49e-05 | 0.7426 |
ZNF525 | 8.2 | 1.965e-09 | 3.4e-05 | 0.8638 |
AASDHPPT | 6.39 | 7.869e-09 | 0.000136 | 0.834 |
VWDE | 6.17 | 1.567e-08 | 0.000271 | 0.7787 |
CGB2 | -6.77 | 1.643e-08 | 0.000284 | 0.8468 |
NEOADJUVANT.THERAPY | Labels | N |
NO | 4 | |
YES | 95 | |
Significant markers | N = 219 | |
Higher in YES | 130 | |
Higher in NO | 89 |
T(pos if higher in 'YES') | ttestP | Q | AUC | |
---|---|---|---|---|
METT10D | 12.14 | 3.578e-21 | 6.2e-17 | 0.9105 |
DSG3 | -12.04 | 1.097e-20 | 1.9e-16 | 0.9895 |
KLHL33 | -11.71 | 2.916e-20 | 5.05e-16 | 0.9132 |
ALDH3A2 | -11.23 | 3.532e-19 | 6.12e-15 | 0.9816 |
KCTD18 | 11.69 | 1.714e-17 | 2.97e-13 | 0.9421 |
HSD17B14 | 12.69 | 9.774e-17 | 1.69e-12 | 0.9947 |
ARV1 | 14.36 | 2.383e-16 | 4.13e-12 | 0.9947 |
TTC13 | 14.36 | 2.383e-16 | 4.13e-12 | 0.9947 |
RRM1 | 10.5 | 1.372e-15 | 2.38e-11 | 0.8658 |
PPP3R1 | 9.81 | 2.695e-15 | 4.67e-11 | 0.8553 |
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Expresson data file = PRAD.meth.for_correlation.filtered_data.txt
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Clinical data file = PRAD.clin.merged.picked.txt
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Number of patients = 99
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Number of genes = 17322
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Number of clinical features = 3
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.