This pipeline uses various statistical tests to identify genes whose promoter methylation levels correlated to selected clinical features.
Testing the association between 20197 genes and 7 clinical features across 114 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 2 clinical features related to at least one genes.
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7 genes correlated to 'GENDER'.
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KIF4B , SDHD , TIMM8B , RELB , EBF2 , ...
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1 gene correlated to 'RACE'.
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CCDC104
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No genes correlated to 'Time to Death', 'AGE', 'KARNOFSKY.PERFORMANCE.SCORE', 'HISTOLOGICAL.TYPE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.
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=0 | ||||
AGE | Spearman correlation test | N=0 | ||||
GENDER | Wilcoxon test | N=7 | male | N=7 | female | N=0 |
KARNOFSKY PERFORMANCE SCORE | Spearman correlation test | N=0 | ||||
HISTOLOGICAL TYPE | Kruskal-Wallis test | N=0 | ||||
RADIATIONS RADIATION REGIMENINDICATION | Wilcoxon test | N=0 | ||||
RACE | Wilcoxon test | N=1 | white | N=1 | black or african american | N=0 |
Time to Death | Duration (Months) | 0.2-58.8 (median=7.4) |
censored | N = 42 | |
death | N = 72 | |
Significant markers | N = 0 |
AGE | Mean (SD) | 60.89 (12) |
Significant markers | N = 0 |
GENDER | Labels | N |
FEMALE | 49 | |
MALE | 65 | |
Significant markers | N = 7 | |
Higher in MALE | 7 | |
Higher in FEMALE | 0 |
No gene related to 'KARNOFSKY.PERFORMANCE.SCORE'.
KARNOFSKY.PERFORMANCE.SCORE | Mean (SD) | 76.75 (15) |
Significant markers | N = 0 |
HISTOLOGICAL.TYPE | Labels | N |
GLIOBLASTOMA MULTIFORME (GBM) | 8 | |
TREATED PRIMARY GBM | 1 | |
UNTREATED PRIMARY (DE NOVO) GBM | 105 | |
Significant markers | N = 0 |
No gene related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 78 | |
YES | 36 | |
Significant markers | N = 0 |
RACE | Labels | N |
BLACK OR AFRICAN AMERICAN | 12 | |
WHITE | 95 | |
Significant markers | N = 1 | |
Higher in WHITE | 1 | |
Higher in BLACK OR AFRICAN AMERICAN | 0 |
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Expresson data file = GBM-TP.meth.by_min_clin_corr.data.txt
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Clinical data file = GBM-TP.merged_data.txt
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Number of patients = 114
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Number of genes = 20197
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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 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 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 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.