Correlation between miRseq expression and clinical features
Rectum Adenocarcinoma (Primary solid tumor)
15 July 2014 | analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1CV4GJK
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/C1CV4GJK
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 427 miRs and 12 clinical features across 143 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 4 clinical features related to at least one miRs.

- 1 miR correlated to 'AGE'.

- HSA-MIR-31

- 8 miRs correlated to 'PATHOLOGY.T.STAGE'.

- HSA-MIR-7-1 , HSA-MIR-548J , HSA-MIR-25 , HSA-MIR-329-2 , HSA-MIR-1274B , ...

- 3 miRs correlated to 'PATHOLOGY.N.STAGE'.

- HSA-MIR-218-1 , HSA-MIR-545 , HSA-MIR-511-2

- 1 miR correlated to 'HISTOLOGICAL.TYPE'.

- HSA-MIR-375

- No miRs correlated to 'Time to Death', 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.M.STAGE', 'GENDER', 'RADIATIONS.RADIATION.REGIMENINDICATION', 'COMPLETENESS.OF.RESECTION', 'NUMBER.OF.LYMPH.NODES', 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 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 |
--- | --- | --- | --- | --- | --- | ---
Time to Death | Cox regression test | N=0 |  |  |  |
AGE | Spearman correlation test | N=1 | older | N=0 | younger | N=1
NEOPLASM DISEASESTAGE | Kruskal-Wallis test | N=0 |  |  |  |
PATHOLOGY T STAGE | Spearman correlation test | N=8 | higher stage | N=0 | lower stage | N=8
PATHOLOGY N STAGE | Spearman correlation test | N=3 | higher stage | N=0 | lower stage | N=3
PATHOLOGY M STAGE | Kruskal-Wallis test | N=0 |  |  |  |
GENDER | Wilcoxon test | N=0 |  |  |  |
HISTOLOGICAL TYPE | Wilcoxon test | N=1 | rectal mucinous adenocarcinoma | N=1 | rectal adenocarcinoma | N=0
RADIATIONS RADIATION REGIMENINDICATION | Wilcoxon test | N=0 |  |  |  |
COMPLETENESS OF RESECTION | Kruskal-Wallis test | N=0 |  |  |  |
NUMBER OF LYMPH NODES | Spearman correlation test | N=0 |  |  |  |
RACE | Kruskal-Wallis test | N=0 |  |  |  |

Clinical variable #1: 'Time to Death'

No miR related to 'Time to Death'.

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

Time to Death | Duration (Months) | 0.2-129.3 (median=15)
| censored | N = 110
| death | N = 21
| Significant markers | N = 0

Clinical variable #2: 'AGE'

One miR related to 'AGE'.

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

AGE | Mean (SD) | 65.41 (11)
| Significant markers | N = 1
| pos. correlated | 0
| neg. correlated | 1

List of one miR differentially expressed by 'AGE'

Table S3. Get Full Table List of one miR significantly correlated to 'AGE' by Spearman correlation test

| SpearmanCorr | corrP | Q
--- | --- | --- | ---
HSA-MIR-31 | -0.307 | 0.0002019 | 0.0862

Clinical variable #3: 'NEOPLASM.DISEASESTAGE'

No miR related to 'NEOPLASM.DISEASESTAGE'.

Table S4. Basic characteristics of clinical feature: 'NEOPLASM.DISEASESTAGE'

NEOPLASM.DISEASESTAGE | Labels | N
| STAGE I | 28
| STAGE II | 8
| STAGE IIA | 33
| STAGE IIB | 2
| STAGE IIC | 1
| STAGE III | 6
| STAGE IIIA | 5
| STAGE IIIB | 20
| STAGE IIIC | 13
| STAGE IV | 15
| STAGE IVA | 7
| Significant markers | N = 0

Clinical variable #4: 'PATHOLOGY.T.STAGE'

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

Table S5. Basic characteristics of clinical feature: 'PATHOLOGY.T.STAGE'

PATHOLOGY.T.STAGE | Mean (SD) | 2.76 (0.67)
|  | N
| 1 | 9
| 2 | 26
| 3 | 97
| 4 | 10
| Significant markers | N = 8
| pos. correlated | 0
| neg. correlated | 8

List of 8 miRs differentially expressed by 'PATHOLOGY.T.STAGE'

Table S6. Get Full Table List of 8 miRs significantly correlated to 'PATHOLOGY.T.STAGE' by Spearman correlation test

| SpearmanCorr | corrP | Q
--- | --- | --- | ---
HSA-MIR-7-1 | -0.3087 | 0.0001853 | 0.0791
HSA-MIR-548J | -0.4267 | 0.0001854 | 0.0791
HSA-MIR-25 | -0.3005 | 0.0002801 | 0.119
HSA-MIR-329-2 | -0.35 | 0.0002894 | 0.123
HSA-MIR-1274B | -0.2985 | 0.0003577 | 0.151
HSA-MIR-451 | -0.293 | 0.0004027 | 0.17
HSA-MIR-144 | -0.2882 | 0.0005059 | 0.213
HSA-MIR-486 | -0.2808 | 0.0007136 | 0.3

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

3 miRs related to 'PATHOLOGY.N.STAGE'.

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

PATHOLOGY.N.STAGE | Mean (SD) | 0.67 (0.79)
|  | N
| 0 | 74
| 1 | 38
| 2 | 28
| Significant markers | N = 3
| pos. correlated | 0
| neg. correlated | 3

List of 3 miRs differentially expressed by 'PATHOLOGY.N.STAGE'

Table S8. Get Full Table List of 3 miRs significantly correlated to 'PATHOLOGY.N.STAGE' by Spearman correlation test

| SpearmanCorr | corrP | Q
--- | --- | --- | ---
HSA-MIR-218-1 | -0.4497 | 0.0001931 | 0.0825
HSA-MIR-545 | -0.3055 | 0.0004544 | 0.194
HSA-MIR-511-2 | -0.2842 | 0.0006977 | 0.297

Clinical variable #6: 'PATHOLOGY.M.STAGE'

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

Table S9. Basic characteristics of clinical feature: 'PATHOLOGY.M.STAGE'

PATHOLOGY.M.STAGE | Labels | N
| M0 | 107
| M1 | 18
| M1A | 2
| MX | 14
| Significant markers | N = 0

Clinical variable #7: 'GENDER'

No miR related to 'GENDER'.

Table S10. Basic characteristics of clinical feature: 'GENDER'

GENDER | Labels | N
| FEMALE | 66
| MALE | 77
| Significant markers | N = 0

Clinical variable #8: 'HISTOLOGICAL.TYPE'

One miR related to 'HISTOLOGICAL.TYPE'.

Table S11. Basic characteristics of clinical feature: 'HISTOLOGICAL.TYPE'

HISTOLOGICAL.TYPE | Labels | N
| RECTAL ADENOCARCINOMA | 127
| RECTAL MUCINOUS ADENOCARCINOMA | 10
| Significant markers | N = 1
| Higher in RECTAL MUCINOUS ADENOCARCINOMA | 1
| Higher in RECTAL ADENOCARCINOMA | 0

List of one miR differentially expressed by 'HISTOLOGICAL.TYPE'

Table S12. Get Full Table List of one miR differentially expressed by 'HISTOLOGICAL.TYPE'

| W(pos if higher in 'RECTAL MUCINOUS ADENOCARCINOMA') | wilcoxontestP | Q | AUC
--- | --- | --- | --- | ---
HSA-MIR-375 | 1102 | 0.0001133 | 0.0462 | 0.8677

Clinical variable #9: 'RADIATIONS.RADIATION.REGIMENINDICATION'

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

Table S13. Basic characteristics of clinical feature: 'RADIATIONS.RADIATION.REGIMENINDICATION'

RADIATIONS.RADIATION.REGIMENINDICATION | Labels | N
| NO | 6
| YES | 137
| Significant markers | N = 0

Clinical variable #10: 'COMPLETENESS.OF.RESECTION'

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

Table S14. Basic characteristics of clinical feature: 'COMPLETENESS.OF.RESECTION'

COMPLETENESS.OF.RESECTION | Labels | N
| R0 | 102
| R1 | 2
| R2 | 11
| RX | 4
| Significant markers | N = 0

Clinical variable #11: 'NUMBER.OF.LYMPH.NODES'

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

Table S15. Basic characteristics of clinical feature: 'NUMBER.OF.LYMPH.NODES'

NUMBER.OF.LYMPH.NODES | Mean (SD) | 2.58 (5.3)
| Significant markers | N = 0

Clinical variable #12: 'RACE'

No miR related to 'RACE'.

Table S16. Basic characteristics of clinical feature: 'RACE'

RACE | Labels | N
| ASIAN | 1
| BLACK OR AFRICAN AMERICAN | 3
| WHITE | 67
| Significant markers | N = 0

Methods & Data
Input

- Expresson data file = READ-TP.miRseq_RPKM_log2.txt

- Clinical data file = READ-TP.merged_data.txt

- Number of patients = 143

- Number of miRs = 427

- Number of clinical features = 12

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

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.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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] Howell, D, Statistical Methods for Psychology. (5th ed.), Duxbury Press:324-5 (2002)
[4] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[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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