Correlation between miRseq expression and clinical features
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 531 miRs and 14 clinical features across 474 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 13 clinical features related to at least one miRs.

  • 1 miR correlated to 'Time to Death'.

    • HSA-MIR-3615

  • 7 miRs correlated to 'AGE'.

    • HSA-MIR-9-2 ,  HSA-MIR-9-1 ,  HSA-MIR-629 ,  HSA-MIR-130B ,  HSA-MIR-29C ,  ...

  • 3 miRs correlated to 'NEOPLASM.DISEASESTAGE'.

    • HSA-MIR-150 ,  HSA-MIR-101-2 ,  HSA-MIR-598

  • 18 miRs correlated to 'PATHOLOGY.T.STAGE'.

    • HSA-MIR-30C-2 ,  HSA-MIR-146A ,  HSA-MIR-101-2 ,  HSA-MIR-150 ,  HSA-MIR-451 ,  ...

  • 5 miRs correlated to 'PATHOLOGY.N.STAGE'.

    • HSA-MIR-200A ,  HSA-MIR-548B ,  HSA-MIR-200B ,  HSA-MIR-181C ,  HSA-MIR-29C

  • 5 miRs correlated to 'PATHOLOGY.M.STAGE'.

    • HSA-MIR-16-1 ,  HSA-MIR-628 ,  HSA-MIR-374A ,  HSA-MIR-181C ,  HSA-MIR-424

  • 10 miRs correlated to 'GENDER'.

    • HSA-MIR-105-2 ,  HSA-MIR-99A ,  HSA-MIR-105-1 ,  HSA-MIR-30E ,  HSA-MIR-361 ,  ...

  • 1 miR correlated to 'KARNOFSKY.PERFORMANCE.SCORE'.

    • HSA-MIR-940

  • 8 miRs correlated to 'HISTOLOGICAL.TYPE'.

    • HSA-MIR-130B ,  HSA-MIR-656 ,  HSA-MIR-18A ,  HSA-MIR-1976 ,  HSA-MIR-369 ,  ...

  • 3 miRs correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

    • HSA-MIR-143 ,  HSA-MIR-181B-2 ,  HSA-MIR-1229

  • 12 miRs correlated to 'NUMBERPACKYEARSSMOKED'.

    • HSA-MIR-339 ,  HSA-MIR-210 ,  HSA-MIR-345 ,  HSA-MIR-296 ,  HSA-MIR-31 ,  ...

  • 2 miRs correlated to 'COMPLETENESS.OF.RESECTION'.

    • HSA-MIR-34B ,  HSA-MIR-34A

  • 1 miR correlated to 'RACE'.

    • HSA-MIR-1304

  • No miRs correlated to '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
Time to Death Cox regression test N=1 shorter survival N=0 longer survival N=1
AGE Spearman correlation test N=7 older N=1 younger N=6
NEOPLASM DISEASESTAGE Kruskal-Wallis test N=3        
PATHOLOGY T STAGE Spearman correlation test N=18 higher stage N=2 lower stage N=16
PATHOLOGY N STAGE Spearman correlation test N=5 higher stage N=0 lower stage N=5
PATHOLOGY M STAGE Kruskal-Wallis test N=5        
GENDER Wilcoxon test N=10 male N=10 female N=0
KARNOFSKY PERFORMANCE SCORE Spearman correlation test N=1 higher score N=0 lower score N=1
HISTOLOGICAL TYPE Kruskal-Wallis test N=8        
RADIATIONS RADIATION REGIMENINDICATION Wilcoxon test N=3 yes N=3 no N=0
NUMBERPACKYEARSSMOKED Spearman correlation test N=12 higher numberpackyearssmoked N=12 lower numberpackyearssmoked N=0
COMPLETENESS OF RESECTION Kruskal-Wallis test N=2        
RACE Kruskal-Wallis test N=1        
ETHNICITY Wilcoxon test   N=0        
Clinical variable #1: 'Time to Death'

One miR related to 'Time to Death'.

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

Time to Death Duration (Years) 1-6443 (median=476)
  censored N = 329
  death N = 86
     
  Significant markers N = 1
  associated with shorter survival 0
  associated with longer survival 1
List of one miR differentially expressed by 'Time to Death'

Table S2.  Get Full Table List of one miR significantly associated with 'Time to Death' by Cox regression test

HazardRatio Wald_P Q C_index
HSA-MIR-3615 0.66 0.0003544 0.19 0.378
Clinical variable #2: 'AGE'

7 miRs related to 'AGE'.

Table S3.  Basic characteristics of clinical feature: 'AGE'

AGE Mean (SD) 65.45 (9.8)
  Significant markers N = 7
  pos. correlated 1
  neg. correlated 6
List of 7 miRs differentially expressed by 'AGE'

Table S4.  Get Full Table List of 7 miRs significantly correlated to 'AGE' by Spearman correlation test

SpearmanCorr corrP Q
HSA-MIR-9-2 -0.1899 5.657e-05 0.03
HSA-MIR-9-1 -0.187 7.33e-05 0.0388
HSA-MIR-629 -0.1777 0.0001667 0.0882
HSA-MIR-130B -0.1755 0.0002025 0.107
HSA-MIR-29C 0.1719 0.000273 0.144
HSA-MIR-937 -0.1697 0.0003495 0.184
HSA-MIR-183 -0.1682 0.0003726 0.196
Clinical variable #3: 'NEOPLASM.DISEASESTAGE'

3 miRs related to 'NEOPLASM.DISEASESTAGE'.

Table S5.  Basic characteristics of clinical feature: 'NEOPLASM.DISEASESTAGE'

NEOPLASM.DISEASESTAGE Labels N
  STAGE I 5
  STAGE IA 115
  STAGE IB 133
  STAGE IIA 49
  STAGE IIB 68
  STAGE IIIA 69
  STAGE IIIB 11
  STAGE IV 23
     
  Significant markers N = 3
List of 3 miRs differentially expressed by 'NEOPLASM.DISEASESTAGE'

Table S6.  Get Full Table List of 3 miRs differentially expressed by 'NEOPLASM.DISEASESTAGE'

ANOVA_P Q
HSA-MIR-150 0.0002615 0.139
HSA-MIR-101-2 0.0005015 0.266
HSA-MIR-598 0.0005346 0.283
Clinical variable #4: 'PATHOLOGY.T.STAGE'

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

Table S7.  Basic characteristics of clinical feature: 'PATHOLOGY.T.STAGE'

PATHOLOGY.T.STAGE Mean (SD) 1.86 (0.73)
  N
  1 146
  2 264
  3 43
  4 18
     
  Significant markers N = 18
  pos. correlated 2
  neg. correlated 16
List of top 10 miRs differentially expressed by 'PATHOLOGY.T.STAGE'

Table S8.  Get Full Table List of top 10 miRs significantly correlated to 'PATHOLOGY.T.STAGE' by Spearman correlation test

SpearmanCorr corrP Q
HSA-MIR-30C-2 -0.2158 2.282e-06 0.00121
HSA-MIR-146A -0.2135 2.927e-06 0.00155
HSA-MIR-101-2 -0.2118 3.532e-06 0.00187
HSA-MIR-150 -0.2066 6.149e-06 0.00325
HSA-MIR-451 -0.2044 7.801e-06 0.00411
HSA-MIR-342 -0.1821 7.039e-05 0.037
HSA-MIR-218-2 -0.1817 7.295e-05 0.0383
HSA-MIR-486 -0.1815 7.48e-05 0.0392
HSA-MIR-374B -0.1811 7.7e-05 0.0403
HSA-MIR-598 -0.1772 0.0001127 0.0588
Clinical variable #5: 'PATHOLOGY.N.STAGE'

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

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

PATHOLOGY.N.STAGE Mean (SD) 0.52 (0.77)
  N
  0 299
  1 90
  2 72
  3 2
     
  Significant markers N = 5
  pos. correlated 0
  neg. correlated 5
List of 5 miRs differentially expressed by 'PATHOLOGY.N.STAGE'

Table S10.  Get Full Table List of 5 miRs significantly correlated to 'PATHOLOGY.N.STAGE' by Spearman correlation test

SpearmanCorr corrP Q
HSA-MIR-200A -0.1767 0.0001321 0.0701
HSA-MIR-548B -0.1817 0.0001438 0.0762
HSA-MIR-200B -0.1691 0.0002578 0.136
HSA-MIR-181C -0.169 0.0002602 0.137
HSA-MIR-29C -0.1662 0.0003282 0.173
Clinical variable #6: 'PATHOLOGY.M.STAGE'

5 miRs related to 'PATHOLOGY.M.STAGE'.

Table S11.  Basic characteristics of clinical feature: 'PATHOLOGY.M.STAGE'

PATHOLOGY.M.STAGE Labels N
  M0 324
  M1 16
  M1A 1
  M1B 4
  MX 125
     
  Significant markers N = 5
List of 5 miRs differentially expressed by 'PATHOLOGY.M.STAGE'

Table S12.  Get Full Table List of 5 miRs differentially expressed by 'PATHOLOGY.M.STAGE'

ANOVA_P Q
HSA-MIR-16-1 3.174e-05 0.0169
HSA-MIR-628 4.323e-05 0.0229
HSA-MIR-374A 0.0001126 0.0595
HSA-MIR-181C 0.0002397 0.127
HSA-MIR-424 0.0002419 0.127
Clinical variable #7: 'GENDER'

10 miRs related to 'GENDER'.

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

GENDER Labels N
  FEMALE 254
  MALE 220
     
  Significant markers N = 10
  Higher in MALE 10
  Higher in FEMALE 0
List of 10 miRs differentially expressed by 'GENDER'

Table S14.  Get Full Table List of 10 miRs 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-105-2 13919 2.913e-06 0.00155 0.659
HSA-MIR-99A 21848 4.207e-05 0.0223 0.609
HSA-MIR-105-1 14402 7.555e-05 0.04 0.6317
HSA-MIR-30E 22343 0.0001679 0.0887 0.6002
HSA-MIR-361 22390 0.0001904 0.1 0.5993
HSA-MIR-133A-1 21470 0.0003013 0.158 0.5973
HSA-MIR-542 22687 0.0004129 0.217 0.594
HSA-MIR-3934 22490 0.0004195 0.22 0.5941
HSA-MIR-1247 22418 0.0004612 0.241 0.5935
HSA-MIR-651 21901 0.0005541 0.289 0.5928
Clinical variable #8: 'KARNOFSKY.PERFORMANCE.SCORE'

One miR related to 'KARNOFSKY.PERFORMANCE.SCORE'.

Table S15.  Basic characteristics of clinical feature: 'KARNOFSKY.PERFORMANCE.SCORE'

KARNOFSKY.PERFORMANCE.SCORE Mean (SD) 83.49 (23)
  Significant markers N = 1
  pos. correlated 0
  neg. correlated 1
List of one miR differentially expressed by 'KARNOFSKY.PERFORMANCE.SCORE'

Table S16.  Get Full Table List of one miR significantly correlated to 'KARNOFSKY.PERFORMANCE.SCORE' by Spearman correlation test

SpearmanCorr corrP Q
HSA-MIR-940 -0.3792 0.0004424 0.235
Clinical variable #9: 'HISTOLOGICAL.TYPE'

8 miRs related to 'HISTOLOGICAL.TYPE'.

Table S17.  Basic characteristics of clinical feature: 'HISTOLOGICAL.TYPE'

HISTOLOGICAL.TYPE Labels N
  LUNG ACINAR ADENOCARCINOMA 15
  LUNG ADENOCARCINOMA MIXED SUBTYPE 93
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) 303
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS 5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS 19
  LUNG CLEAR CELL ADENOCARCINOMA 2
  LUNG MICROPAPILLARY ADENOCARCINOMA 3
  LUNG MUCINOUS ADENOCARCINOMA 2
  LUNG PAPILLARY ADENOCARCINOMA 19
  LUNG SIGNET RING ADENOCARCINOMA 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA 5
  MUCINOUS (COLLOID) CARCINOMA 7
     
  Significant markers N = 8
List of 8 miRs differentially expressed by 'HISTOLOGICAL.TYPE'

Table S18.  Get Full Table List of 8 miRs differentially expressed by 'HISTOLOGICAL.TYPE'

ANOVA_P Q
HSA-MIR-130B 3.597e-05 0.0191
HSA-MIR-656 0.0001126 0.0597
HSA-MIR-18A 0.0001305 0.069
HSA-MIR-1976 0.0002004 0.106
HSA-MIR-369 0.0002443 0.129
HSA-LET-7B 0.0004407 0.232
HSA-MIR-200B 0.0005493 0.288
HSA-MIR-133A-1 0.0005698 0.299
Clinical variable #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

3 miRs related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

Table S19.  Basic characteristics of clinical feature: 'RADIATIONS.RADIATION.REGIMENINDICATION'

RADIATIONS.RADIATION.REGIMENINDICATION Labels N
  NO 20
  YES 454
     
  Significant markers N = 3
  Higher in YES 3
  Higher in NO 0
List of 3 miRs differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

Table S20.  Get Full Table List of 3 miRs differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

W(pos if higher in 'YES') wilcoxontestP Q AUC
HSA-MIR-143 2270 0.0001534 0.0813 0.75
HSA-MIR-181B-2 6731 0.0002584 0.137 0.7413
HSA-MIR-1229 4473 0.0005371 0.284 0.7556
Clinical variable #11: 'NUMBERPACKYEARSSMOKED'

12 miRs related to 'NUMBERPACKYEARSSMOKED'.

Table S21.  Basic characteristics of clinical feature: 'NUMBERPACKYEARSSMOKED'

NUMBERPACKYEARSSMOKED Mean (SD) 42.22 (27)
  Significant markers N = 12
  pos. correlated 12
  neg. correlated 0
List of top 10 miRs differentially expressed by 'NUMBERPACKYEARSSMOKED'

Table S22.  Get Full Table List of top 10 miRs significantly correlated to 'NUMBERPACKYEARSSMOKED' by Spearman correlation test

SpearmanCorr corrP Q
HSA-MIR-339 0.2468 6.762e-06 0.00359
HSA-MIR-210 0.2448 8.059e-06 0.00427
HSA-MIR-345 0.2313 2.533e-05 0.0134
HSA-MIR-296 0.2292 3.112e-05 0.0164
HSA-MIR-31 0.219 0.0001011 0.0533
HSA-MIR-590 0.2049 0.0001999 0.105
HSA-MIR-1295 0.231 0.0002048 0.108
HSA-MIR-130A 0.2036 0.0002193 0.115
HSA-MIR-136 0.1971 0.0003516 0.184
HSA-MIR-199B 0.1941 0.0004334 0.226
Clinical variable #12: 'COMPLETENESS.OF.RESECTION'

2 miRs related to 'COMPLETENESS.OF.RESECTION'.

Table S23.  Basic characteristics of clinical feature: 'COMPLETENESS.OF.RESECTION'

COMPLETENESS.OF.RESECTION Labels N
  R0 324
  R1 12
  R2 4
  RX 21
     
  Significant markers N = 2
List of 2 miRs differentially expressed by 'COMPLETENESS.OF.RESECTION'

Table S24.  Get Full Table List of 2 miRs differentially expressed by 'COMPLETENESS.OF.RESECTION'

ANOVA_P Q
HSA-MIR-34B 0.0002343 0.124
HSA-MIR-34A 0.0004461 0.236
Clinical variable #13: 'RACE'

One miR related to 'RACE'.

Table S25.  Basic characteristics of clinical feature: 'RACE'

RACE Labels N
  ASIAN 7
  BLACK OR AFRICAN AMERICAN 35
  WHITE 365
     
  Significant markers N = 1
List of one miR differentially expressed by 'RACE'

Table S26.  Get Full Table List of one miR differentially expressed by 'RACE'

ANOVA_P Q
HSA-MIR-1304 0.0002214 0.118
Clinical variable #14: 'ETHNICITY'

No miR related to 'ETHNICITY'.

Table S27.  Basic characteristics of clinical feature: 'ETHNICITY'

ETHNICITY Labels N
  HISPANIC OR LATINO 7
  NOT HISPANIC OR LATINO 343
     
  Significant markers N = 0
Methods & Data
Input

  • Expresson data file = LUAD-TP.miRseq_RPKM_log2.txt

  • Clinical data file = LUAD-TP.merged_data.txt

  • Number of patients = 474

  • Number of miRs = 531

  • Number of clinical features = 14

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.

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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