(WT cohort)
This pipeline uses various statistical tests to identify genes whose promoter methylation levels correlated to selected clinical features.
Testing the association between 17162 genes and 6 clinical features across 18 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 'PRIMARY.SITE.OF.DISEASE'.
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FAP , SLC4A10
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100 genes correlated to 'LYMPH.NODE.METASTASIS'.
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VSTM2B , FAHD2B , STARD4 , FOXC2 , CHRNB2 , ...
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111 genes correlated to 'NEOPLASM.DISEASESTAGE'.
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HSPA1B , SLC25A39 , GPR142 , VSTM2B , C18ORF18 , ...
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No genes correlated to 'Time to Death', 'AGE', and 'GENDER'.
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=0 | ||||
PRIMARY SITE OF DISEASE | ANOVA test | N=2 | ||||
GENDER | t test | N=0 | ||||
LYMPH NODE METASTASIS | ANOVA test | N=100 | ||||
NEOPLASM DISEASESTAGE | ANOVA test | N=111 |
Time to Death | Duration (Months) | 4.9-78.4 (median=13) |
censored | N = 2 | |
death | N = 7 | |
Significant markers | N = 0 |
AGE | Mean (SD) | 58.5 (15) |
Significant markers | N = 0 |
PRIMARY.SITE.OF.DISEASE | Labels | N |
DISTANT METASTASIS | 3 | |
REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS) | 3 | |
REGIONAL LYMPH NODE | 12 | |
Significant markers | N = 2 |
GENDER | Labels | N |
FEMALE | 9 | |
MALE | 9 | |
Significant markers | N = 0 |
LYMPH.NODE.METASTASIS | Labels | N |
N0 | 9 | |
N1 | 1 | |
N1A | 1 | |
N1B | 3 | |
N2B | 1 | |
N3 | 1 | |
Significant markers | N = 100 |
ANOVA_P | Q | |
---|---|---|
VSTM2B | 4.344e-18 | 7.45e-14 |
FAHD2B | 4.316e-17 | 7.41e-13 |
STARD4 | 2.526e-16 | 4.34e-12 |
FOXC2 | 2.693e-13 | 4.62e-09 |
CHRNB2 | 4.69e-13 | 8.05e-09 |
CPNE8 | 4.958e-13 | 8.51e-09 |
PUS3 | 6.23e-13 | 1.07e-08 |
FAM53B | 6.821e-13 | 1.17e-08 |
MGC12982 | 8.858e-13 | 1.52e-08 |
GAB4 | 9.716e-13 | 1.67e-08 |
NEOPLASM.DISEASESTAGE | Labels | N |
STAGE I | 4 | |
STAGE IA | 1 | |
STAGE II | 1 | |
STAGE IIB | 1 | |
STAGE IIC | 2 | |
STAGE III | 1 | |
STAGE IIIA | 1 | |
STAGE IIIB | 1 | |
STAGE IIIC | 3 | |
Significant markers | N = 111 |
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Expresson data file = SKCM-WT.meth.for_correlation.filtered_data.txt
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Clinical data file = SKCM-WT.clin.merged.picked.txt
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Number of patients = 18
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Number of genes = 17162
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Number of clinical features = 6
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.