This pipeline uses various statistical tests to identify genes whose promoter methylation levels correlated to selected clinical features.
Testing the association between 17584 genes and 5 clinical features across 220 samples, statistically thresholded by Q value < 0.05, 4 clinical features related to at least one genes.
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4 genes correlated to 'Time to Death'.
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TMEM84 , MIB2 , SLC38A8 , DUSP5P
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100 genes correlated to 'AGE'.
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SLFN14 , ACAA2 , SCARNA17 , PLA2G15 , ALS2CL , ...
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1350 genes correlated to 'HISTOLOGICAL.TYPE'.
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ARL13B , UBE2T , CARD11 , CRYAB , NCRNA00203 , ...
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4 genes correlated to 'NEOADJUVANT.THERAPY'.
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DNAH3 , C1GALT1 , RG9MTD3 , LOC647979
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No genes correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'
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=4 | shorter survival | N=0 | longer survival | N=4 |
AGE | Spearman correlation test | N=100 | older | N=32 | younger | N=68 |
HISTOLOGICAL TYPE | ANOVA test | N=1350 | ||||
RADIATIONS RADIATION REGIMENINDICATION | t test | N=0 | ||||
NEOADJUVANT THERAPY | t test | N=4 | yes | N=4 | no | N=0 |
Time to Death | Duration (Months) | 0-187.1 (median=13.2) |
censored | N = 202 | |
death | N = 17 | |
Significant markers | N = 4 | |
associated with shorter survival | 0 | |
associated with longer survival | 4 |
HazardRatio | Wald_P | Q | C_index | |
---|---|---|---|---|
TMEM84 | 0 | 1.359e-07 | 0.0024 | 0.367 |
MIB2 | 0 | 2.42e-07 | 0.0043 | 0.377 |
SLC38A8 | 0 | 1.518e-06 | 0.027 | 0.392 |
DUSP5P | 0.01 | 2.2e-06 | 0.039 | 0.365 |
AGE | Mean (SD) | 63.5 (11) |
Significant markers | N = 100 | |
pos. correlated | 32 | |
neg. correlated | 68 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
SLFN14 | 0.4229 | 5.889e-11 | 1.04e-06 |
ACAA2 | -0.4176 | 1.077e-10 | 1.89e-06 |
SCARNA17 | -0.4176 | 1.077e-10 | 1.89e-06 |
PLA2G15 | -0.4043 | 4.663e-10 | 8.2e-06 |
ALS2CL | -0.3994 | 7.845e-10 | 1.38e-05 |
LOC100271836 | -0.3872 | 2.792e-09 | 4.91e-05 |
ADAMTS15 | -0.3843 | 3.731e-09 | 6.56e-05 |
GPR160 | -0.3793 | 6.134e-09 | 0.000108 |
CYP1A2 | 0.375 | 9.43e-09 | 0.000166 |
EPS8L2 | -0.3738 | 1.052e-08 | 0.000185 |
HISTOLOGICAL.TYPE | Labels | N |
ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | 168 | |
ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | 4 | |
ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) | 1 | |
ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | 3 | |
MIXED SEROUS AND ENDOMETRIOID | 9 | |
SEROUS ENDOMETRIAL ADENOCARCINOMA | 35 | |
Significant markers | N = 1350 |
ANOVA_P | Q | |
---|---|---|
ARL13B | 2.554e-133 | 4.49e-129 |
UBE2T | 2.135e-90 | 3.75e-86 |
CARD11 | 1.218e-32 | 2.14e-28 |
CRYAB | 6.58e-29 | 1.16e-24 |
NCRNA00203 | 3.494e-27 | 6.14e-23 |
ABCB6 | 4.201e-27 | 7.38e-23 |
APBB1IP | 5.983e-27 | 1.05e-22 |
KCNIP2 | 7.495e-26 | 1.32e-21 |
SSTR1 | 1.241e-25 | 2.18e-21 |
ADAMTS8 | 2.015e-25 | 3.54e-21 |
No gene related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 62 | |
YES | 158 | |
Significant markers | N = 0 |
NEOADJUVANT.THERAPY | Labels | N |
NO | 60 | |
YES | 160 | |
Significant markers | N = 4 | |
Higher in YES | 4 | |
Higher in NO | 0 |
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Expresson data file = UCEC.meth.for_correlation.filtered_data.txt
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Clinical data file = UCEC.clin.merged.picked.txt
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Number of patients = 220
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Number of genes = 17584
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Number of clinical features = 5
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.