Correlation between mRNAseq expression and clinical features
Prostate Adenocarcinoma (Primary solid tumor)
21 April 2013 | analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C1WM1BCS
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Prostate Adenocarcinoma (Primary solid tumor cohort) - 21 April 2013: Correlation between mRNAseq expression and clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1WM1BCS
Overview
Introduction

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

Summary

Testing the association between 18257 genes and 4 clinical features across 153 samples, statistically thresholded by Q value < 0.05, 3 clinical features related to at least one genes.

- 1 gene correlated to 'AGE'.

- ADAP2|55803

- 30 genes correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- C14ORF126|112487 , CEBPZ|10153 , ABHD11|83451 , SFRS2|6427 , MCOLN2|255231 , ...

- 1 gene correlated to 'COMPLETENESS.OF.RESECTION'.

- GLP2R|9340

- No genes correlated to 'NUMBER.OF.LYMPH.NODES'

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 |
--- | --- | --- | --- | --- | --- | ---
AGE | Spearman correlation test | N=1 | older | N=1 | younger | N=0
RADIATIONS RADIATION REGIMENINDICATION | t test | N=30 | yes | N=8 | no | N=22
COMPLETENESS OF RESECTION | ANOVA test | N=1 |  |  |  |
NUMBER OF LYMPH NODES | Spearman correlation test | N=0 |  |  |  |

Clinical variable #1: 'AGE'

One gene related to 'AGE'.

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

AGE | Mean (SD) | 60.49 (6.9)
| Significant markers | N = 1
| pos. correlated | 1
| neg. correlated | 0

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

Table S2. Get Full Table List of one gene significantly correlated to 'AGE' by Spearman correlation test

| SpearmanCorr | corrP | Q
--- | --- | --- | ---
ADAP2|55803 | 0.388 | 7.87e-07 | 0.0144

Figure S1. Get High-res Image As an example, this figure shows the association of ADAP2|55803 to 'AGE'. P value = 7.87e-07 with Spearman correlation analysis. The straight line presents the best linear regression.

Clinical variable #2: 'RADIATIONS.RADIATION.REGIMENINDICATION'

30 genes related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

Table S3. Basic characteristics of clinical feature: 'RADIATIONS.RADIATION.REGIMENINDICATION'

RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N
| NO | 5
| YES | 148
| Significant markers | N = 30
| Higher in YES | 8
| Higher in NO | 22

List of top 10 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

Table S4. Get Full Table List of top 10 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

| T(pos if higher in 'YES') | ttestP | Q | AUC
--- | --- | --- | --- | ---
C14ORF126|112487 | -10.72 | 3.125e-17 | 5.47e-13 | 0.8527
CEBPZ|10153 | -10.55 | 2.889e-16 | 5.05e-12 | 0.8554
ABHD11|83451 | 12.03 | 4.211e-12 | 7.37e-08 | 0.9108
SFRS2|6427 | -10.08 | 3.636e-11 | 6.36e-07 | 0.8392
MCOLN2|255231 | -7.14 | 1.947e-10 | 3.41e-06 | 0.7054
CDC40|51362 | -9.28 | 3.636e-10 | 6.36e-06 | 0.8514
TMEM161B|153396 | -8.76 | 2.362e-09 | 4.13e-05 | 0.8851
SFRS13A|10772 | -9.78 | 3.218e-09 | 5.63e-05 | 0.873
ABCD1|215 | 8.33 | 3.263e-09 | 5.71e-05 | 0.8122
PPIG|9360 | -7.15 | 4.42e-09 | 7.73e-05 | 0.7095

Figure S2. Get High-res Image As an example, this figure shows the association of C14ORF126|112487 to 'RADIATIONS.RADIATION.REGIMENINDICATION'. P value = 3.13e-17 with T-test analysis.

Clinical variable #3: 'COMPLETENESS.OF.RESECTION'

One gene related to 'COMPLETENESS.OF.RESECTION'.

Table S5. Basic characteristics of clinical feature: 'COMPLETENESS.OF.RESECTION'

COMPLETENESS.OF.RESECTION | Labels | N
| R0 | 117
| R1 | 29
| RX | 2
| Significant markers | N = 1

List of one gene differentially expressed by 'COMPLETENESS.OF.RESECTION'

Table S6. Get Full Table List of one gene differentially expressed by 'COMPLETENESS.OF.RESECTION'

| ANOVA_P | Q
--- | --- | ---
GLP2R|9340 | 9.218e-10 | 1.68e-05

Figure S3. Get High-res Image As an example, this figure shows the association of GLP2R|9340 to 'COMPLETENESS.OF.RESECTION'. P value = 9.22e-10 with ANOVA analysis.

Clinical variable #4: 'NUMBER.OF.LYMPH.NODES'

No gene related to 'NUMBER.OF.LYMPH.NODES'.

Table S7. Basic characteristics of clinical feature: 'NUMBER.OF.LYMPH.NODES'

NUMBER.OF.LYMPH.NODES | Mean (SD) | 0.21 (0.74)
| Significant markers | N = 0

Methods & Data
Input

- Expresson data file = PRAD-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

- Clinical data file = PRAD-TP.clin.merged.picked.txt

- Number of patients = 153

- Number of genes = 18257

- Number of clinical features = 4

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.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Spearman, C, The proof and measurement of association between two things, Amer. J. Psychol 15:72-101 (1904)
[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] Howell, D, Statistical Methods for Psychology. (5th ed.), Duxbury Press:324-5 (2002)
[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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