Correlation between mRNAseq expression and clinical features
Rectum Adenocarcinoma (Primary solid tumor)
23 May 2013 | analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1RR1W9N
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between mRNAseq expression and clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1RR1W9N
Overview
Introduction

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

Summary

Testing the association between 18106 genes and 8 clinical features across 51 samples, statistically thresholded by Q value < 0.05, 3 clinical features related to at least one genes.

- 14 genes correlated to 'GENDER'.

- DDX3Y|8653 , ZFY|7544 , XIST|7503 , EIF1AY|9086 , PRKY|5616 , ...

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

- GUSBL2|375513 , TTC15|51112 , GNG3|2785 , RMND5B|64777 , ZNF608|57507 , ...

- 2 genes correlated to 'NEOPLASM.DISEASESTAGE'.

- METT11D1|64745 , UBE2E3|10477

- No genes correlated to 'AGE', 'DISTANT.METASTASIS', 'LYMPH.NODE.METASTASIS', 'COMPLETENESS.OF.RESECTION', and '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=0 |  |  |  |
GENDER | t test | N=14 | male | N=12 | female | N=2
RADIATIONS RADIATION REGIMENINDICATION | t test | N=47 | yes | N=15 | no | N=32
DISTANT METASTASIS | ANOVA test | N=0 |  |  |  |
LYMPH NODE METASTASIS | ANOVA test | N=0 |  |  |  |
COMPLETENESS OF RESECTION | ANOVA test | N=0 |  |  |  |
NUMBER OF LYMPH NODES | Spearman correlation test | N=0 |  |  |  |
NEOPLASM DISEASESTAGE | ANOVA test | N=2 |  |  |  |

Clinical variable #1: 'AGE'

No gene related to 'AGE'.

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

AGE | Mean (SD) | 63.33 (12)
| Significant markers | N = 0

Clinical variable #2: 'GENDER'

14 genes related to 'GENDER'.

Table S2. Basic characteristics of clinical feature: 'GENDER'

GENDER | Labels | N
| FEMALE | 23
| MALE | 28
| Significant markers | N = 14
| Higher in MALE | 12
| Higher in FEMALE | 2

List of top 10 genes differentially expressed by 'GENDER'

Table S3. Get Full Table List of top 10 genes differentially expressed by 'GENDER'

| T(pos if higher in 'MALE') | ttestP | Q | AUC
--- | --- | --- | --- | ---
DDX3Y|8653 | 31.09 | 9.353e-26 | 1.69e-21 | 1
ZFY|7544 | 26.85 | 3.725e-25 | 6.74e-21 | 1
XIST|7503 | -19.94 | 1.177e-24 | 2.13e-20 | 1
EIF1AY|9086 | 24.06 | 7.095e-22 | 1.28e-17 | 1
PRKY|5616 | 15.42 | 6.024e-20 | 1.09e-15 | 1
USP9Y|8287 | 22.78 | 1.041e-18 | 1.88e-14 | 1
CYORF15A|246126 | 19.49 | 1.387e-18 | 2.51e-14 | 1
KDM5D|8284 | 27.37 | 5.082e-18 | 9.19e-14 | 1
RPS4Y1|6192 | 17.83 | 9.967e-17 | 1.8e-12 | 1
CYORF15B|84663 | 15.97 | 8.844e-15 | 1.6e-10 | 1

Figure S1. Get High-res Image As an example, this figure shows the association of DDX3Y|8653 to 'GENDER'. P value = 9.35e-26 with T-test analysis.

Clinical variable #3: 'RADIATIONS.RADIATION.REGIMENINDICATION'

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

Table S4. Basic characteristics of clinical feature: 'RADIATIONS.RADIATION.REGIMENINDICATION'

RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N
| NO | 3
| YES | 48
| Significant markers | N = 47
| Higher in YES | 15
| Higher in NO | 32

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

Table S5. Get Full Table List of top 10 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

| T(pos if higher in 'YES') | ttestP | Q | AUC
--- | --- | --- | --- | ---
GUSBL2|375513 | -9.35 | 2.16e-12 | 3.57e-08 | 0.8819
TTC15|51112 | 8.72 | 1.792e-11 | 2.96e-07 | 0.9028
GNG3|2785 | -8.59 | 3.078e-11 | 5.09e-07 | 0.8958
RMND5B|64777 | 8.67 | 1.021e-10 | 1.69e-06 | 0.9306
ZNF608|57507 | 8.54 | 2.098e-10 | 3.47e-06 | 0.8958
PAK1IP1|55003 | -7.92 | 5.672e-10 | 9.38e-06 | 0.9236
DDX19A|55308 | -7.64 | 7.938e-10 | 1.31e-05 | 0.8681
TRA2B|6434 | -7.76 | 2.197e-09 | 3.63e-05 | 0.8889
WASH2P|375260 | -7.16 | 3.865e-09 | 6.39e-05 | 0.8542
TMEM117|84216 | -7.15 | 4.477e-09 | 7.4e-05 | 0.8681

Figure S2. Get High-res Image As an example, this figure shows the association of GUSBL2|375513 to 'RADIATIONS.RADIATION.REGIMENINDICATION'. P value = 2.16e-12 with T-test analysis.

Clinical variable #4: 'DISTANT.METASTASIS'

No gene related to 'DISTANT.METASTASIS'.

Table S6. Basic characteristics of clinical feature: 'DISTANT.METASTASIS'

DISTANT.METASTASIS | Labels | N
| M0 | 37
| M1 | 4
| M1A | 1
| MX | 9
| Significant markers | N = 0

Clinical variable #5: 'LYMPH.NODE.METASTASIS'

No gene related to 'LYMPH.NODE.METASTASIS'.

Table S7. Basic characteristics of clinical feature: 'LYMPH.NODE.METASTASIS'

LYMPH.NODE.METASTASIS | Labels | N
| N0 | 26
| N1 | 6
| N1A | 1
| N1B | 3
| N2 | 8
| N2B | 5
| NX | 2
| Significant markers | N = 0

Clinical variable #6: 'COMPLETENESS.OF.RESECTION'

No gene related to 'COMPLETENESS.OF.RESECTION'.

Table S8. Basic characteristics of clinical feature: 'COMPLETENESS.OF.RESECTION'

COMPLETENESS.OF.RESECTION | Labels | N
| R0 | 35
| R1 | 1
| RX | 3
| Significant markers | N = 0

Clinical variable #7: 'NUMBER.OF.LYMPH.NODES'

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

Table S9. Basic characteristics of clinical feature: 'NUMBER.OF.LYMPH.NODES'

NUMBER.OF.LYMPH.NODES | Mean (SD) | 3.18 (5.9)
| Significant markers | N = 0

Clinical variable #8: 'NEOPLASM.DISEASESTAGE'

2 genes related to 'NEOPLASM.DISEASESTAGE'.

Table S10. Basic characteristics of clinical feature: 'NEOPLASM.DISEASESTAGE'

NEOPLASM.DISEASESTAGE | Labels | N
| STAGE I | 11
| STAGE II | 2
| STAGE IIA | 10
| STAGE IIB | 1
| STAGE IIC | 1
| STAGE IIIA | 4
| STAGE IIIB | 5
| STAGE IIIC | 7
| STAGE IV | 2
| STAGE IVA | 5
| Significant markers | N = 2

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

Table S11. Get Full Table List of 2 genes differentially expressed by 'NEOPLASM.DISEASESTAGE'

| ANOVA_P | Q
--- | --- | ---
METT11D1|64745 | 5.441e-07 | 0.00985
UBE2E3|10477 | 8.896e-07 | 0.0161

Figure S3. Get High-res Image As an example, this figure shows the association of METT11D1|64745 to 'NEOPLASM.DISEASESTAGE'. P value = 5.44e-07 with ANOVA analysis.

Methods & Data
Input

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

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

- Number of patients = 51

- Number of genes = 18106

- Number of clinical features = 8

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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