Correlation between gene methylation status and clinical features

Overview

Introduction

This pipeline uses various statistical tests to identify genes whose promoter methylation levels correlated to selected clinical features.

Summary

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.

7 genes correlated to 'GENDER'.

KIF4B , SDHD , TIMM8B , RELB , EBF2 , ...

1 gene correlated to 'RACE'.

CCDC104

No genes correlated to 'Time to Death', 'AGE', 'KARNOFSKY.PERFORMANCE.SCORE', 'HISTOLOGICAL.TYPE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

Results

Overview of the results

Complete statistical result table is provided in Supplement Table 1

Table 1. Get Full Table This table shows the clinical features, statistical methods used, and the number of genes that are significantly associated with each clinical feature at P value < 0.05 and Q value < 0.3.

Clinical feature	Statistical test	Significant genes	Associated with		Associated with
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

Clinical variable #1: 'Time to Death'

No gene related to 'Time to Death'.

Table S1. Basic characteristics of clinical feature: 'Time to Death'


Time to Death	Duration (Months)	0.2-58.8 (median=7.4)
	censored	N = 42
	death	N = 72

	Significant markers	N = 0

Clinical variable #2: 'AGE'

No gene related to 'AGE'.

Table S2. Basic characteristics of clinical feature: 'AGE'


AGE	Mean (SD)	60.89 (12)
	Significant markers	N = 0

Clinical variable #3: 'GENDER'

7 genes related to 'GENDER'.

Table S3. Basic characteristics of clinical feature: 'GENDER'


GENDER	Labels	N
	FEMALE	49
	MALE	65

	Significant markers	N = 7
	Higher in MALE	7
	Higher in FEMALE	0

List of 7 genes differentially expressed by 'GENDER'

Table S4. Get Full Table List of 7 genes differentially expressed by 'GENDER'. 0 significant gene(s) located in sex chromosomes is(are) filtered out.

	W(pos if higher in 'MALE')	wilcoxontestP	Q	AUC
KIF4B	570	4.923e-09	9.94e-05	0.821
SDHD	2460	6.957e-07	0.0141	0.7724
TIMM8B	2460	6.957e-07	0.0141	0.7724
RELB	2423	2.026e-06	0.0409	0.7608
EBF2	2374	7.81e-06	0.158	0.7454
CDH20	829	1.258e-05	0.254	0.7397
FRG1B	834	1.434e-05	0.289	0.7381

Clinical variable #4: 'KARNOFSKY.PERFORMANCE.SCORE'

No gene related to 'KARNOFSKY.PERFORMANCE.SCORE'.

Table S5. Basic characteristics of clinical feature: 'KARNOFSKY.PERFORMANCE.SCORE'


KARNOFSKY.PERFORMANCE.SCORE	Mean (SD)	76.75 (15)
	Significant markers	N = 0

Clinical variable #5: 'HISTOLOGICAL.TYPE'

No gene related to 'HISTOLOGICAL.TYPE'.

Table S6. Basic characteristics of clinical feature: 'HISTOLOGICAL.TYPE'


HISTOLOGICAL.TYPE	Labels	N
	GLIOBLASTOMA MULTIFORME (GBM)	8
	TREATED PRIMARY GBM	1
	UNTREATED PRIMARY (DE NOVO) GBM	105

	Significant markers	N = 0

Clinical variable #6: 'RADIATIONS.RADIATION.REGIMENINDICATION'

No gene related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

Table S7. Basic characteristics of clinical feature: 'RADIATIONS.RADIATION.REGIMENINDICATION'


RADIATIONS.RADIATION.REGIMENINDICATION	Labels	N
	NO	78
	YES	36

	Significant markers	N = 0

Clinical variable #7: 'RACE'

One gene related to 'RACE'.

Table S8. Basic characteristics of clinical feature: 'RACE'


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

List of one gene differentially expressed by 'RACE'

Table S9. Get Full Table List of one gene differentially expressed by 'RACE'

	W(pos if higher in 'WHITE')	wilcoxontestP	Q	AUC
CCDC104	124	1.092e-05	0.22	0.8912

Methods & Data

Input

Expresson data file = GBM-TP.meth.by_min_clin_corr.data.txt
Clinical data file = GBM-TP.merged_data.txt
Number of patients = 114
Number of genes = 20197
Number of clinical features = 7

Survival analysis

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

Correlation analysis

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

Student's t-test analysis

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

ANOVA analysis

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

Q value calculation

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.

References

[1] Andersen and Gill, Cox's regression model for counting processes, a large sample study, Annals of Statistics 10(4):1100-1120 (1982)

[2] Spearman, C, The proof and measurement of association between two things, Amer. J. Psychol 15:72-101 (1904)

[3] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)

[4] Howell, D, Statistical Methods for Psychology. (5th ed.), Duxbury Press:324-5 (2002)

[5] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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