Brain Lower Grade Glioma: Correlation between miRseq expression and clinical features

Maintained by Juok Cho (Broad Institute)

Overview

Introduction

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

Summary

Testing the association between 560 genes and 7 clinical features across 160 samples, statistically thresholded by Q value < 0.05, 4 clinical features related to at least one genes.

4 genes correlated to 'Time to Death'.

HSA-MIR-10A , HSA-MIR-346 , HSA-MIR-155 , HSA-MIR-15B

1 gene correlated to 'AGE'.

HSA-MIR-195

28 genes correlated to 'HISTOLOGICAL.TYPE'.

HSA-MIR-1262 , HSA-MIR-186 , HSA-MIR-3074 , HSA-MIR-23A , HSA-MIR-455 , ...

1 gene correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

HSA-MIR-1262

No genes correlated to 'GENDER', 'KARNOFSKY.PERFORMANCE.SCORE', 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 genes that are significantly associated with each clinical feature at Q value < 0.05.

Clinical feature	Statistical test	Significant genes	Associated with		Associated with
Time to Death	Cox regression test	N=4	shorter survival	N=3	longer survival	N=1
AGE	Spearman correlation test	N=1	older	N=1	younger	N=0
GENDER	t test	N=0
KARNOFSKY PERFORMANCE SCORE	Spearman correlation test	N=0
HISTOLOGICAL TYPE	ANOVA test	N=28
RADIATIONS RADIATION REGIMENINDICATION	t test	N=1	yes	N=0	no	N=1
NEOADJUVANT THERAPY	t test	N=0

Clinical variable #1: 'Time to Death'

4 genes related to 'Time to Death'.

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


Time to Death	Duration (Months)	0-211.2 (median=17.4)
	censored	N = 111
	death	N = 48

	Significant markers	N = 4
	associated with shorter survival	3
	associated with longer survival	1

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

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

	HazardRatio	Wald_P	Q	C_index
HSA-MIR-10A	1.45	4.4e-08	2.5e-05	0.72
HSA-MIR-346	0.52	4.794e-08	2.7e-05	0.293
HSA-MIR-155	1.84	2.771e-07	0.00015	0.742
HSA-MIR-15B	1.7	1.372e-05	0.0076	0.775

Figure S1. Get High-res Image As an example, this figure shows the association of HSA-MIR-10A to 'Time to Death'. four curves present the cumulative survival rates of 4 quartile subsets of patients. P value = 4.4e-08 with univariate Cox regression analysis using continuous log-2 expression values.

Clinical variable #2: 'AGE'

One gene related to 'AGE'.

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


AGE	Mean (SD)	43.48 (13)
	Significant markers	N = 1
	pos. correlated	1
	neg. correlated	0

List of one gene significantly correlated to 'AGE' by Spearman correlation test

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

	SpearmanCorr	corrP	Q
HSA-MIR-195	0.3172	4.381e-05	0.0245

Figure S2. Get High-res Image As an example, this figure shows the association of HSA-MIR-195 to 'AGE'. P value = 4.38e-05 with Spearman correlation analysis. The straight line presents the best linear regression.

Clinical variable #3: 'GENDER'

No gene related to 'GENDER'.

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


GENDER	Labels	N
	FEMALE	68
	MALE	92

	Significant markers	N = 0

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

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

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


KARNOFSKY.PERFORMANCE.SCORE	Mean (SD)	89 (11)
	Significant markers	N = 0

Clinical variable #5: 'HISTOLOGICAL.TYPE'

28 genes related to 'HISTOLOGICAL.TYPE'.

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


HISTOLOGICAL.TYPE	Labels	N
	ASTROCYTOMA	53
	OLIGOASTROCYTOMA	39
	OLIGODENDROGLIOMA	67

	Significant markers	N = 28

List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'

Table S8. Get Full Table List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'

	ANOVA_P	Q
HSA-MIR-1262	3.679e-11	2.06e-08
HSA-MIR-186	4.893e-08	2.73e-05
HSA-MIR-3074	5.264e-08	2.94e-05
HSA-MIR-23A	5.95e-08	3.31e-05
HSA-MIR-455	1.003e-07	5.58e-05
HSA-MIR-3127	2.805e-07	0.000156
HSA-MIR-1226	9.253e-07	0.000513
HSA-MIR-576	3.299e-06	0.00182
HSA-MIR-3923	3.772e-06	0.00208
HSA-MIR-2114	6.665e-06	0.00367

Figure S3. Get High-res Image As an example, this figure shows the association of HSA-MIR-1262 to 'HISTOLOGICAL.TYPE'. P value = 3.68e-11 with ANOVA analysis.

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

One gene related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

Table S9. Basic characteristics of clinical feature: 'RADIATIONS.RADIATION.REGIMENINDICATION'


RADIATIONS.RADIATION.REGIMENINDICATION	Labels	N
	NO	94
	YES	66

	Significant markers	N = 1
	Higher in YES	0
	Higher in NO	1

List of one gene differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

Table S10. Get Full Table List of one gene differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

	T(pos if higher in 'YES')	ttestP	Q	AUC
HSA-MIR-1262	-4.34	2.759e-05	0.0155	0.7031

Figure S4. Get High-res Image As an example, this figure shows the association of HSA-MIR-1262 to 'RADIATIONS.RADIATION.REGIMENINDICATION'. P value = 2.76e-05 with T-test analysis.

Clinical variable #7: 'NEOADJUVANT.THERAPY'

No gene related to 'NEOADJUVANT.THERAPY'.

Table S11. Basic characteristics of clinical feature: 'NEOADJUVANT.THERAPY'


NEOADJUVANT.THERAPY	Labels	N
	NO	78
	YES	82

	Significant markers	N = 0

Methods & Data

Input

Expresson data file = LGG.miRseq_RPKM_log2.txt
Clinical data file = LGG.clin.merged.picked.txt
Number of patients = 160
Number of genes = 560
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.

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] 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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