This pipeline uses various statistical tests to identify genes whose promoter methylation levels correlated to selected clinical features.
Testing the association between 19998 genes and 9 clinical features across 160 samples, statistically thresholded by Q value < 0.05, 4 clinical features related to at least one genes.
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1 gene correlated to 'AGE'.
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RARB
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62 genes correlated to 'PATHOLOGY.M.STAGE'.
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DUOX2 , DUOXA2 , TANC1 , LRCH1 , DPYD , ...
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1940 genes correlated to 'HISTOLOGICAL.TYPE'.
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SETD7 , HORMAD1 , CIDEA , ANO6__1 , PLEKHA9 , ...
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21 genes correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
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C22ORF26__1 , LOC150381__1 , TMEM160 , CWC22 , C12ORF51 , ...
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No genes correlated to 'Time to Death', 'PATHOLOGY.T.STAGE', 'PATHOLOGY.N.STAGE', 'NUMBERPACKYEARSSMOKED', and 'NUMBER.OF.LYMPH.NODES'.
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=1 | older | N=0 | younger | N=1 |
PATHOLOGY T STAGE | Spearman correlation test | N=0 | ||||
PATHOLOGY N STAGE | t test | N=0 | ||||
PATHOLOGY M STAGE | ANOVA test | N=62 | ||||
HISTOLOGICAL TYPE | ANOVA test | N=1940 | ||||
RADIATIONS RADIATION REGIMENINDICATION | t test | N=21 | yes | N=7 | no | N=14 |
NUMBERPACKYEARSSMOKED | Spearman correlation test | N=0 | ||||
NUMBER OF LYMPH NODES | Spearman correlation test | N=0 |
Time to Death | Duration (Months) | 0-177 (median=12.7) |
censored | N = 121 | |
death | N = 32 | |
Significant markers | N = 0 |
AGE | Mean (SD) | 47.79 (13) |
Significant markers | N = 1 | |
pos. correlated | 0 | |
neg. correlated | 1 |
SpearmanCorr | corrP | Q | |
---|---|---|---|
RARB | -0.44 | 6.531e-09 | 0.000131 |
PATHOLOGY.T.STAGE | Mean (SD) | 1.34 (0.6) |
N | ||
1 | 87 | |
2 | 31 | |
3 | 2 | |
4 | 2 | |
Significant markers | N = 0 |
PATHOLOGY.N.STAGE | Labels | N |
class0 | 79 | |
class1 | 39 | |
Significant markers | N = 0 |
PATHOLOGY.M.STAGE | Labels | N |
M0 | 68 | |
M1 | 3 | |
MX | 55 | |
Significant markers | N = 62 |
ANOVA_P | Q | |
---|---|---|
DUOX2 | 3.459e-16 | 6.92e-12 |
DUOXA2 | 3.459e-16 | 6.92e-12 |
TANC1 | 5.904e-13 | 1.18e-08 |
LRCH1 | 1.232e-12 | 2.46e-08 |
DPYD | 4.852e-12 | 9.7e-08 |
C17ORF75 | 2.104e-11 | 4.21e-07 |
NEK9 | 2.325e-11 | 4.65e-07 |
FIGNL1 | 4.248e-11 | 8.49e-07 |
SERHL2 | 1.141e-10 | 2.28e-06 |
HSPA1A__1 | 1.796e-10 | 3.59e-06 |
HISTOLOGICAL.TYPE | Labels | N |
ADENOSQUAMOUS | 2 | |
CERVICAL SQUAMOUS CELL CARCINOMA | 134 | |
ENDOCERVICAL ADENOCARCINOMA OF THE USUAL TYPE | 4 | |
ENDOCERVICAL TYPE OF ADENOCARCINOMA | 16 | |
ENDOMETRIOID ADENOCARCINOMA OF ENDOCERVIX | 1 | |
MUCINOUS ADENOCARCINOMA OF ENDOCERVICAL TYPE | 3 | |
Significant markers | N = 1940 |
ANOVA_P | Q | |
---|---|---|
SETD7 | 1.577e-107 | 3.15e-103 |
HORMAD1 | 4.041e-99 | 8.08e-95 |
CIDEA | 6.654e-90 | 1.33e-85 |
ANO6__1 | 2.209e-86 | 4.42e-82 |
PLEKHA9 | 2.209e-86 | 4.42e-82 |
PACS1 | 7.271e-68 | 1.45e-63 |
FAM71D | 8.693e-54 | 1.74e-49 |
PTGIR | 6.31e-46 | 1.26e-41 |
ATP10D | 3.279e-45 | 6.55e-41 |
CYP27C1 | 1.963e-42 | 3.92e-38 |
21 genes related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N |
NO | 30 | |
YES | 130 | |
Significant markers | N = 21 | |
Higher in YES | 7 | |
Higher in NO | 14 |
T(pos if higher in 'YES') | ttestP | Q | AUC | |
---|---|---|---|---|
C22ORF26__1 | -6.89 | 1.057e-08 | 0.000211 | 0.8333 |
LOC150381__1 | -6.89 | 1.057e-08 | 0.000211 | 0.8333 |
TMEM160 | 6.05 | 1.576e-08 | 0.000315 | 0.7472 |
CWC22 | 5.88 | 2.475e-08 | 0.000495 | 0.7792 |
C12ORF51 | -6.05 | 2.809e-08 | 0.000562 | 0.7764 |
ANKRD5 | 5.87 | 3.229e-08 | 0.000646 | 0.7564 |
ZFP91__1 | 6.13 | 3.266e-08 | 0.000653 | 0.7778 |
ZFP91-CNTF__2 | 6.13 | 3.266e-08 | 0.000653 | 0.7778 |
ZYG11B | -6.11 | 2.092e-07 | 0.00418 | 0.8023 |
BTC | -6.18 | 2.172e-07 | 0.00434 | 0.8372 |
NUMBERPACKYEARSSMOKED | Mean (SD) | 18.44 (12) |
Significant markers | N = 0 |
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Expresson data file = CESC-TP.meth.by_min_clin_corr.data.txt
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Clinical data file = CESC-TP.merged_data.txt
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Number of patients = 160
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Number of genes = 19998
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Number of clinical features = 9
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.