This pipeline uses various statistical tests to identify genes whose promoter methylation levels correlated to selected clinical features.
Testing the association between 20302 genes and 7 clinical features across 397 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 4 clinical features related to at least one genes.
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406 genes correlated to 'AGE'.
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ANGPT4 , GPR158 , ALS2CL , EPB41L1 , SLFN14 , ...
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4098 genes correlated to 'HISTOLOGICAL.TYPE'.
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APBB1IP , RASGRF1 , SSTR1 , LRRC36__1 , KCNA5 , ...
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69 genes correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
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RMND5B , ZNF831 , GOLGA3 , MAP2K2 , SAP130 , ...
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46 genes correlated to 'RACE'.
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C18ORF54 , GNB2L1 , SNORD95 , GRAPL , NCRNA00174 , ...
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No genes correlated to 'Time to Death', 'COMPLETENESS.OF.RESECTION', and 'ETHNICITY'.
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=406 | older | N=149 | younger | N=257 |
HISTOLOGICAL TYPE | Kruskal-Wallis test | N=4098 | ||||
RADIATIONS RADIATION REGIMENINDICATION | Wilcoxon test | N=69 | yes | N=69 | no | N=0 |
COMPLETENESS OF RESECTION | Kruskal-Wallis test | N=0 | ||||
RACE | Kruskal-Wallis test | N=46 | ||||
ETHNICITY | Wilcoxon test | N=0 |
Time to Death | Duration (Months) | 0-191.8 (median=18.2) |
censored | N = 350 | |
death | N = 45 | |
Significant markers | N = 0 |
AGE | Mean (SD) | 64.01 (11) |
Significant markers | N = 406 | |
pos. correlated | 149 | |
neg. correlated | 257 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
ANGPT4 | 0.3493 | 8.294e-13 | 1.68e-08 |
GPR158 | -0.3313 | 1.346e-11 | 2.73e-07 |
ALS2CL | -0.3222 | 5.155e-11 | 1.05e-06 |
EPB41L1 | -0.3186 | 8.636e-11 | 1.75e-06 |
SLFN14 | 0.3153 | 1.371e-10 | 2.78e-06 |
CTSG | 0.3116 | 2.297e-10 | 4.66e-06 |
PLA2G15 | -0.3112 | 2.435e-10 | 4.94e-06 |
CACNB1 | -0.3111 | 2.477e-10 | 5.03e-06 |
ITPK1 | -0.3088 | 3.371e-10 | 6.84e-06 |
NCRNA00203 | -0.3088 | 3.371e-10 | 6.84e-06 |
HISTOLOGICAL.TYPE | Labels | N |
ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | 288 | |
MIXED SEROUS AND ENDOMETRIOID | 20 | |
SEROUS ENDOMETRIAL ADENOCARCINOMA | 89 | |
Significant markers | N = 4098 |
69 genes related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 87 | |
YES | 310 | |
Significant markers | N = 69 | |
Higher in YES | 69 | |
Higher in NO | 0 |
W(pos if higher in 'YES') | wilcoxontestP | Q | AUC | |
---|---|---|---|---|
RMND5B | 18908 | 9.847e-09 | 2e-04 | 0.7011 |
ZNF831 | 18891 | 1.095e-08 | 0.000222 | 0.7004 |
GOLGA3 | 18880 | 1.172e-08 | 0.000238 | 0.7 |
MAP2K2 | 18773 | 2.263e-08 | 0.000459 | 0.6961 |
SAP130 | 18720 | 3.12e-08 | 0.000633 | 0.6941 |
C14ORF93 | 18639 | 5.067e-08 | 0.00103 | 0.6911 |
GIPR | 18618 | 5.74e-08 | 0.00116 | 0.6903 |
TMEM125 | 18572 | 7.528e-08 | 0.00153 | 0.6886 |
GUSBL2 | 18530 | 9.624e-08 | 0.00195 | 0.6871 |
C11ORF2 | 18364 | 2.494e-07 | 0.00506 | 0.6809 |
COMPLETENESS.OF.RESECTION | Labels | N |
R0 | 265 | |
R1 | 18 | |
R2 | 13 | |
RX | 29 | |
Significant markers | N = 0 |
RACE | Labels | N |
AMERICAN INDIAN OR ALASKA NATIVE | 2 | |
ASIAN | 7 | |
BLACK OR AFRICAN AMERICAN | 82 | |
NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER | 7 | |
WHITE | 277 | |
Significant markers | N = 46 |
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Expresson data file = UCEC-TP.meth.by_min_clin_corr.data.txt
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Clinical data file = UCEC-TP.merged_data.txt
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Number of patients = 397
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Number of genes = 20302
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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.
In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.