Glioblastoma Multiforme: Correlation between miR expression and clinical features

Maintained by TCGA GDAC Team (Broad Institute/Dana-Farber Cancer Institute/Harvard Medical School)

Overview

Introduction

This pipeline uses various statistical tests to identify miRs whose expression levels correlated to selected clinical features.

Summary

Testing the association between 534 miRs and 7 clinical features across 482 samples, statistically thresholded by Q value < 0.05, 2 clinical features related to at least one miRs.

4 miRs correlated to 'Time to Death'.

HSA-MIR-222 , HSA-MIR-221 , HSA-MIR-148A , HSA-MIR-34A

3 miRs correlated to 'AGE'.

HSA-MIR-148A , HSA-MIR-210 , HSA-MIR-339

No miRs correlated to 'GENDER', 'KARNOFSKY.PERFORMANCE.SCORE', 'HISTOLOGICAL.TYPE', 'RADIATIONS.RADIATION.REGIMENINDICATION', and 'NEOADJUVANT.THERAPY'.

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 miRs that are significantly associated with each clinical feature at Q value < 0.05.

Clinical feature	Statistical test	Significant miRs	Associated with		Associated with
Time to Death	Cox regression test	N=4	shorter survival	N=4	longer survival	N=0
AGE	Spearman correlation test	N=3	older	N=3	younger	N=0
GENDER	t test	N=0
KARNOFSKY PERFORMANCE SCORE	Spearman correlation test	N=0
HISTOLOGICAL TYPE	t test	N=0
RADIATIONS RADIATION REGIMENINDICATION	t test	N=0
NEOADJUVANT THERAPY	t test	N=0

Clinical variable #1: 'Time to Death'

4 miRs related to 'Time to Death'.

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


Time to Death	Duration (Months)	0.1-127.6 (median=10.3)
	censored	N = 103
	death	N = 379

	Significant markers	N = 4
	associated with shorter survival	4
	associated with longer survival	0

List of 4 miRs significantly associated with 'Time to Death' by Cox regression test

Table S2. Get Full Table List of 4 miRs significantly associated with 'Time to Death' by Cox regression test

	HazardRatio	Wald_P	Q	C_index
HSA-MIR-222	1.27	6.105e-09	3.3e-06	0.563
HSA-MIR-221	1.32	1.292e-06	0.00069	0.554
HSA-MIR-148A	1.21	2.856e-05	0.015	0.564
HSA-MIR-34A	1.2	7.211e-05	0.038	0.54

Figure S1. Get High-res Image As an example, this figure shows the association of HSA-MIR-222 to 'Time to Death'. four curves present the cumulative survival rates of 4 quartile subsets of patients. P value = 6.11e-09 with univariate Cox regression analysis using continuous log-2 expression values.

Clinical variable #2: 'AGE'

3 miRs related to 'AGE'.

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


AGE	Mean (SD)	57.53 (15)
	Significant markers	N = 3
	pos. correlated	3
	neg. correlated	0

List of 3 miRs significantly correlated to 'AGE' by Spearman correlation test

Table S4. Get Full Table List of 3 miRs significantly correlated to 'AGE' by Spearman correlation test

	SpearmanCorr	corrP	Q
HSA-MIR-148A	0.2148	1.933e-06	0.00103
HSA-MIR-210	0.1952	1.587e-05	0.00846
HSA-MIR-339	0.1809	6.511e-05	0.0346

Figure S2. Get High-res Image As an example, this figure shows the association of HSA-MIR-148A to 'AGE'. P value = 1.93e-06 with Spearman correlation analysis. The straight line presents the best linear regression.

Clinical variable #3: 'GENDER'

No miR related to 'GENDER'.

Table S5. Basic characteristics of clinical feature: 'GENDER'


GENDER	Labels	N
	FEMALE	187
	MALE	295

	Significant markers	N = 0

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

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

Table S6. Basic characteristics of clinical feature: 'KARNOFSKY.PERFORMANCE.SCORE'


KARNOFSKY.PERFORMANCE.SCORE	Mean (SD)	77.61 (14)
	Significant markers	N = 0

Clinical variable #5: 'HISTOLOGICAL.TYPE'

No miR related to 'HISTOLOGICAL.TYPE'.

Table S7. Basic characteristics of clinical feature: 'HISTOLOGICAL.TYPE'


HISTOLOGICAL.TYPE	Labels	N
	TREATED PRIMARY GBM	20
	UNTREATED PRIMARY (DE NOVO) GBM	325

	Significant markers	N = 0

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

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

Table S8. Basic characteristics of clinical feature: 'RADIATIONS.RADIATION.REGIMENINDICATION'


RADIATIONS.RADIATION.REGIMENINDICATION	Labels	N
	NO	337
	YES	145

	Significant markers	N = 0

Clinical variable #7: 'NEOADJUVANT.THERAPY'

No miR related to 'NEOADJUVANT.THERAPY'.

Table S9. Basic characteristics of clinical feature: 'NEOADJUVANT.THERAPY'


NEOADJUVANT.THERAPY	Labels	N
	NO	289
	YES	193

	Significant markers	N = 0

Methods & Data

Input

Expresson data file = GBM.mirna__h_mirna_8x15k__unc_edu__Level_3__unc_DWD_Batch_adjusted__data.data.txt
Clinical data file = GBM.clin.merged.picked.txt
Number of patients = 482
Number of miRs = 534
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

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.

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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] 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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