Correlation between mRNAseq expression and clinical features
Pancreatic Adenocarcinoma (Primary solid tumor)
23 May 2013 | analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1S180JR
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/C1S180JR
Overview
Introduction

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

Summary

Testing the association between 18603 genes and 7 clinical features across 18 samples, statistically thresholded by Q value < 0.05, 2 clinical features related to at least one genes.

- 9 genes correlated to 'GENDER'.

- XIST|7503 , NLGN4Y|22829 , ZFY|7544 , RPS4Y1|6192 , UTY|7404 , ...

- 7 genes correlated to 'NEOPLASM.DISEASESTAGE'.

- CCNT1|904 , ZC3HAV1L|92092 , TAF1L|138474 , ZNF192|7745 , UHMK1|127933 , ...

- 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=9 | male | N=6 | female | N=3
DISTANT METASTASIS | ANOVA test | N=0 |  |  |  |
LYMPH NODE METASTASIS | t test | N=0 |  |  |  |
COMPLETENESS OF RESECTION | ANOVA test | N=0 |  |  |  |
NUMBER OF LYMPH NODES | Spearman correlation test | N=0 |  |  |  |
NEOPLASM DISEASESTAGE | ANOVA test | N=7 |  |  |  |

Clinical variable #1: 'AGE'

No gene related to 'AGE'.

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

AGE | Mean (SD) | 64.94 (8.4)
| Significant markers | N = 0

Clinical variable #2: 'GENDER'

9 genes related to 'GENDER'.

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

GENDER | Labels | N
| FEMALE | 10
| MALE | 8
| Significant markers | N = 9
| Higher in MALE | 6
| Higher in FEMALE | 3

List of 9 genes differentially expressed by 'GENDER'

Table S3. Get Full Table List of 9 genes differentially expressed by 'GENDER'

| T(pos if higher in 'MALE') | ttestP | Q | AUC
--- | --- | --- | --- | ---
XIST|7503 | -27.05 | 1.384e-14 | 2.55e-10 | 1
NLGN4Y|22829 | 27.25 | 9.312e-13 | 1.71e-08 | 1
ZFY|7544 | 19.95 | 3.289e-10 | 6.06e-06 | 1
RPS4Y1|6192 | 32.26 | 5.773e-10 | 1.06e-05 | 1
UTY|7404 | 33.87 | 6.866e-10 | 1.26e-05 | 1
PRKY|5616 | 13.28 | 1.188e-09 | 2.19e-05 | 1
DDX3Y|8653 | 26.31 | 2.967e-09 | 5.46e-05 | 1
TSIX|9383 | -18.37 | 1.08e-08 | 0.000199 | 1
HDHD1A|8226 | -7.12 | 2.448e-06 | 0.0451 | 0.9875

Figure S1. Get High-res Image As an example, this figure shows the association of XIST|7503 to 'GENDER'. P value = 1.38e-14 with T-test analysis.

Clinical variable #3: 'DISTANT.METASTASIS'

No gene related to 'DISTANT.METASTASIS'.

Table S4. Basic characteristics of clinical feature: 'DISTANT.METASTASIS'

DISTANT.METASTASIS | Labels | N
| M0 | 3
| M1 | 1
| MX | 14
| Significant markers | N = 0

Clinical variable #4: 'LYMPH.NODE.METASTASIS'

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

Table S5. Basic characteristics of clinical feature: 'LYMPH.NODE.METASTASIS'

LYMPH.NODE.METASTASIS | Labels | N
| N0 | 8
| N1 | 10
| Significant markers | N = 0

Clinical variable #5: 'COMPLETENESS.OF.RESECTION'

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

Table S6. Basic characteristics of clinical feature: 'COMPLETENESS.OF.RESECTION'

COMPLETENESS.OF.RESECTION | Labels | N
| R0 | 13
| R1 | 4
| RX | 1
| Significant markers | N = 0

Clinical variable #6: '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) | 1.78 (2.7)
| Significant markers | N = 0

Clinical variable #7: 'NEOPLASM.DISEASESTAGE'

7 genes related to 'NEOPLASM.DISEASESTAGE'.

Table S8. Basic characteristics of clinical feature: 'NEOPLASM.DISEASESTAGE'

NEOPLASM.DISEASESTAGE | Labels | N
| STAGE IA | 2
| STAGE IB | 1
| STAGE IIA | 3
| STAGE IIB | 10
| STAGE III | 1
| STAGE IV | 1
| Significant markers | N = 7

List of 7 genes differentially expressed by 'NEOPLASM.DISEASESTAGE'

Table S9. Get Full Table List of 7 genes differentially expressed by 'NEOPLASM.DISEASESTAGE'

| ANOVA_P | Q
--- | --- | ---
CCNT1|904 | 1.572e-07 | 0.00292
ZC3HAV1L|92092 | 1.662e-07 | 0.00309
TAF1L|138474 | 3.862e-07 | 0.00718
ZNF192|7745 | 5.154e-07 | 0.00958
UHMK1|127933 | 5.479e-07 | 0.0102
ANKRD36BP1|84832 | 7.551e-07 | 0.014
C19ORF56|51398 | 2.182e-06 | 0.0406

Figure S2. Get High-res Image As an example, this figure shows the association of CCNT1|904 to 'NEOPLASM.DISEASESTAGE'. P value = 1.57e-07 with ANOVA analysis.

Methods & Data
Input

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

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

- Number of patients = 18

- Number of genes = 18603

- Number of clinical features = 7

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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