Correlation between RPPA expression and clinical features

Glioblastoma Multiforme (Primary solid tumor)

17 October 2014 | analyses__2014_10_17

Maintainer Information

Citation Information

Maintained by Juok Cho (Broad Institute)

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between RPPA expression and clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1QF8RR2

Overview

Introduction

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

Summary

Testing the association between 171 genes and 7 clinical features across 211 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 2 clinical features related to at least one genes.

3 genes correlated to 'Time to Death'.

PTGS2|COX-2-R-C , IGFBP2|IGFBP2-R-V , ANXA1|ANNEXIN_I-R-V

1 gene correlated to 'GENDER'.

SHC1|SHC_PY317-R-NA

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

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=3	shorter survival	N=3	longer survival	N=0
AGE	Spearman correlation test	N=0
GENDER	Wilcoxon test	N=1	male	N=1	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	Kruskal-Wallis test	N=0

Clinical variable #1: 'Time to Death'

3 genes related to 'Time to Death'.

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


Time to Death	Duration (Months)	0.1-108.8 (median=8.2)
	censored	N = 52
	death	N = 159

	Significant markers	N = 3
	associated with shorter survival	3
	associated with longer survival	0

List of 3 genes differentially expressed by 'Time to Death'

Table S2. Get Full Table List of 3 genes significantly associated with 'Time to Death' by Cox regression test

	HazardRatio	Wald_P	Q	C_index
PTGS2\|COX-2-R-C	1.46	0.0001421	0.024	0.583
IGFBP2\|IGFBP2-R-V	1.3	0.0003256	0.055	0.578
ANXA1\|ANNEXIN_I-R-V	1.27	0.0004701	0.079	0.552

Clinical variable #2: 'AGE'

No gene related to 'AGE'.

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


AGE	Mean (SD)	59.88 (14)
	Significant markers	N = 0

Clinical variable #3: 'GENDER'

One gene related to 'GENDER'.

Table S4. Basic characteristics of clinical feature: 'GENDER'


GENDER	Labels	N
	FEMALE	85
	MALE	126

	Significant markers	N = 1
	Higher in MALE	1
	Higher in FEMALE	0

List of one gene differentially expressed by 'GENDER'

Table S5. Get Full Table List of one gene 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
SHC1\|SHC_PY317-R-NA	7151	3.663e-05	0.00626	0.6677

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)	75.68 (15)
	Significant markers	N = 0

Clinical variable #5: 'HISTOLOGICAL.TYPE'

No gene related to 'HISTOLOGICAL.TYPE'.

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


HISTOLOGICAL.TYPE	Labels	N
	GLIOBLASTOMA MULTIFORME (GBM)	1
	TREATED PRIMARY GBM	3
	UNTREATED PRIMARY (DE NOVO) GBM	207

	Significant markers	N = 0

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

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

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


RADIATIONS.RADIATION.REGIMENINDICATION	Labels	N
	NO	156
	YES	55

	Significant markers	N = 0

Clinical variable #7: 'RACE'

No gene related to 'RACE'.

Table S9. Basic characteristics of clinical feature: 'RACE'


RACE	Labels	N
	ASIAN	4
	BLACK OR AFRICAN AMERICAN	11
	WHITE	180

	Significant markers	N = 0

Methods & Data

Input

Expresson data file = GBM-TP.rppa.txt
Clinical data file = GBM-TP.merged_data.txt
Number of patients = 211
Number of genes = 171
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

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.

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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