Correlation between miRseq expression and clinical features

Kidney Chromophobe (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 miRseq expression and clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C10G3J13

Overview

Introduction

This pipeline uses various statistical tests to identify miRs whose log2 expression levels correlated to selected clinical features.

Summary

Testing the association between 469 miRs and 10 clinical features across 66 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 5 clinical features related to at least one miRs.

2 miRs correlated to 'NEOPLASM.DISEASESTAGE'.

HSA-MIR-10A , HSA-MIR-181B-1

4 miRs correlated to 'PATHOLOGY.T.STAGE'.

HSA-MIR-181B-1 , HSA-MIR-181A-1 , HSA-MIR-200A , HSA-MIR-429

1 miR correlated to 'GENDER'.

HSA-MIR-219-1

2 miRs correlated to 'KARNOFSKY.PERFORMANCE.SCORE'.

HSA-MIR-7-1 , HSA-MIR-181D

1 miR correlated to 'RACE'.

HSA-MIR-410

No miRs correlated to 'AGE', 'PATHOLOGY.N.STAGE', 'PATHOLOGY.M.STAGE', 'NUMBERPACKYEARSSMOKED', and 'ETHNICITY'.

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 P value < 0.05 and Q value < 0.3.

Clinical feature	Statistical test	Significant miRs	Associated with		Associated with
AGE	Spearman correlation test	N=0
NEOPLASM DISEASESTAGE	Kruskal-Wallis test	N=2
PATHOLOGY T STAGE	Spearman correlation test	N=4	higher stage	N=2	lower stage	N=2
PATHOLOGY N STAGE	Spearman correlation test	N=0
PATHOLOGY M STAGE	Kruskal-Wallis test	N=0
GENDER	Wilcoxon test	N=1	male	N=1	female	N=0
KARNOFSKY PERFORMANCE SCORE	Spearman correlation test	N=2	higher score	N=1	lower score	N=1
NUMBERPACKYEARSSMOKED	Spearman correlation test	N=0
RACE	Kruskal-Wallis test	N=1
ETHNICITY	Wilcoxon test	N=0

Clinical variable #1: 'AGE'

No miR related to 'AGE'.

Table S1. Basic characteristics of clinical feature: 'AGE'


AGE	Mean (SD)	51.52 (14)
	Significant markers	N = 0

Clinical variable #2: 'NEOPLASM.DISEASESTAGE'

2 miRs related to 'NEOPLASM.DISEASESTAGE'.

Table S2. Basic characteristics of clinical feature: 'NEOPLASM.DISEASESTAGE'


NEOPLASM.DISEASESTAGE	Labels	N
	STAGE I	21
	STAGE II	25
	STAGE III	14
	STAGE IV	6

	Significant markers	N = 2

List of 2 miRs differentially expressed by 'NEOPLASM.DISEASESTAGE'

Table S3. Get Full Table List of 2 miRs differentially expressed by 'NEOPLASM.DISEASESTAGE'

	ANOVA_P	Q
HSA-MIR-10A	0.0004293	0.201
HSA-MIR-181B-1	0.0004795	0.224

Clinical variable #3: 'PATHOLOGY.T.STAGE'

4 miRs related to 'PATHOLOGY.T.STAGE'.

Table S4. Basic characteristics of clinical feature: 'PATHOLOGY.T.STAGE'


PATHOLOGY.T.STAGE	Mean (SD)	2.02 (0.85)
		N
	1	21
	2	25
	3	18
	4	2

	Significant markers	N = 4
	pos. correlated	2
	neg. correlated	2

List of 4 miRs differentially expressed by 'PATHOLOGY.T.STAGE'

Table S5. Get Full Table List of 4 miRs significantly correlated to 'PATHOLOGY.T.STAGE' by Spearman correlation test

	SpearmanCorr	corrP	Q
HSA-MIR-181B-1	0.505	1.53e-05	0.00717
HSA-MIR-181A-1	0.445	0.0001813	0.0848
HSA-MIR-200A	-0.4362	0.0002511	0.117
HSA-MIR-429	-0.4218	0.0004198	0.196

Clinical variable #4: 'PATHOLOGY.N.STAGE'

No miR related to 'PATHOLOGY.N.STAGE'.

Table S6. Basic characteristics of clinical feature: 'PATHOLOGY.N.STAGE'


PATHOLOGY.N.STAGE	Mean (SD)	0.16 (0.47)
		N
	0	40
	1	3
	2	2

	Significant markers	N = 0

Clinical variable #5: 'PATHOLOGY.M.STAGE'

No miR related to 'PATHOLOGY.M.STAGE'.

Table S7. Basic characteristics of clinical feature: 'PATHOLOGY.M.STAGE'


PATHOLOGY.M.STAGE	Labels	N
	M0	34
	M1	2
	MX	9

	Significant markers	N = 0

Clinical variable #6: 'GENDER'

One miR related to 'GENDER'.

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


GENDER	Labels	N
	FEMALE	27
	MALE	39

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

List of one miR differentially expressed by 'GENDER'

Table S9. Get Full Table List of one miR 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
HSA-MIR-219-1	638	0.0005136	0.241	0.7705

Clinical variable #7: 'KARNOFSKY.PERFORMANCE.SCORE'

2 miRs related to 'KARNOFSKY.PERFORMANCE.SCORE'.

Table S10. Basic characteristics of clinical feature: 'KARNOFSKY.PERFORMANCE.SCORE'


KARNOFSKY.PERFORMANCE.SCORE	Mean (SD)	89.09 (9.4)
	Score	N
	70	1
	80	2
	90	5
	100	3

	Significant markers	N = 2
	pos. correlated	1
	neg. correlated	1

List of 2 miRs differentially expressed by 'KARNOFSKY.PERFORMANCE.SCORE'

Table S11. Get Full Table List of 2 miRs significantly correlated to 'KARNOFSKY.PERFORMANCE.SCORE' by Spearman correlation test

	SpearmanCorr	corrP	Q
HSA-MIR-7-1	0.9028	0.0001411	0.0645
HSA-MIR-181D	-0.8642	0.0006005	0.274

Clinical variable #8: 'NUMBERPACKYEARSSMOKED'

No miR related to 'NUMBERPACKYEARSSMOKED'.

Table S12. Basic characteristics of clinical feature: 'NUMBERPACKYEARSSMOKED'


NUMBERPACKYEARSSMOKED	Mean (SD)	25.09 (22)
	Significant markers	N = 0

Clinical variable #9: 'RACE'

One miR related to 'RACE'.

Table S13. Basic characteristics of clinical feature: 'RACE'


RACE	Labels	N
	ASIAN	2
	BLACK OR AFRICAN AMERICAN	4
	WHITE	58

	Significant markers	N = 1

List of one miR differentially expressed by 'RACE'

Table S14. Get Full Table List of one miR differentially expressed by 'RACE'

	ANOVA_P	Q
HSA-MIR-410	0.0004995	0.229

Clinical variable #10: 'ETHNICITY'

No miR related to 'ETHNICITY'.

Table S15. Basic characteristics of clinical feature: 'ETHNICITY'


ETHNICITY	Labels	N
	HISPANIC OR LATINO	4
	NOT HISPANIC OR LATINO	32

	Significant markers	N = 0

Methods & Data

Input

Expresson data file = KICH-TP.miRseq_RPKM_log2.txt
Clinical data file = KICH-TP.merged_data.txt
Number of patients = 66
Number of miRs = 469
Number of clinical features = 10

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

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

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

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

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

[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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