Correlation between miRseq expression and clinical features
Thyroid Adenocarcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
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/C16M35SN
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 512 miRs and 17 clinical features across 496 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 16 clinical features related to at least one miRs.

  • 13 miRs correlated to 'Time to Death'.

    • HSA-MIR-376A-1 ,  HSA-MIR-181A-2 ,  HSA-MIR-487A ,  HSA-MIR-425 ,  HSA-MIR-30D ,  ...

  • 18 miRs correlated to 'AGE'.

    • HSA-MIR-625 ,  HSA-MIR-181A-2 ,  HSA-MIR-376A-1 ,  HSA-MIR-3622A ,  HSA-MIR-362 ,  ...

  • 54 miRs correlated to 'NEOPLASM.DISEASESTAGE'.

    • HSA-MIR-139 ,  HSA-MIR-376C ,  HSA-MIR-126 ,  HSA-MIR-154 ,  HSA-MIR-199A-1 ,  ...

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

    • HSA-MIR-139 ,  HSA-MIR-126 ,  HSA-MIR-363 ,  HSA-MIR-3074 ,  HSA-MIR-7-2 ,  ...

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

    • HSA-MIR-21 ,  HSA-MIR-7-2 ,  HSA-MIR-204 ,  HSA-MIR-1179 ,  HSA-MIR-146B ,  ...

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

    • HSA-MIR-3677 ,  HSA-MIR-151 ,  HSA-MIR-655 ,  HSA-MIR-136 ,  HSA-MIR-1274B ,  ...

  • 2 miRs correlated to 'GENDER'.

    • HSA-MIR-651 ,  HSA-MIR-361

  • 206 miRs correlated to 'HISTOLOGICAL.TYPE'.

    • HSA-MIR-21 ,  HSA-MIR-7-2 ,  HSA-MIR-146B ,  HSA-MIR-148B ,  HSA-MIR-511-2 ,  ...

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

    • HSA-MIR-374A ,  HSA-MIR-660 ,  HSA-MIR-130A ,  HSA-MIR-324 ,  HSA-MIR-20B ,  ...

  • 80 miRs correlated to 'EXTRATHYROIDAL.EXTENSION'.

    • HSA-MIR-148B ,  HSA-MIR-21 ,  HSA-MIR-363 ,  HSA-MIR-127 ,  HSA-MIR-376C ,  ...

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

    • HSA-MIR-139 ,  HSA-MIR-196A-1 ,  HSA-MIR-935

  • 69 miRs correlated to 'NUMBER.OF.LYMPH.NODES'.

    • HSA-MIR-7-2 ,  HSA-MIR-21 ,  HSA-MIR-1179 ,  HSA-MIR-511-2 ,  HSA-MIR-382 ,  ...

  • 1 miR correlated to 'MULTIFOCALITY'.

    • HSA-MIR-132

  • 14 miRs correlated to 'TUMOR.SIZE'.

    • HSA-MIR-9-2 ,  HSA-MIR-9-1 ,  HSA-MIR-107 ,  HSA-MIR-183 ,  HSA-MIR-199A-1 ,  ...

  • 6 miRs correlated to 'RACE'.

    • HSA-MIR-3130-1 ,  HSA-MIR-20A ,  HSA-MIR-17 ,  HSA-MIR-3917 ,  HSA-MIR-338 ,  ...

  • 5 miRs correlated to 'ETHNICITY'.

    • HSA-MIR-153-1 ,  HSA-MIR-934 ,  HSA-MIR-34A ,  HSA-MIR-652 ,  HSA-MIR-3690

  • No miRs correlated to 'RADIATIONEXPOSURE'

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=13 shorter survival N=9 longer survival N=4
AGE Spearman correlation test N=18 older N=9 younger N=9
NEOPLASM DISEASESTAGE Kruskal-Wallis test N=54        
PATHOLOGY T STAGE Spearman correlation test N=39 higher stage N=19 lower stage N=20
PATHOLOGY N STAGE Wilcoxon test N=101 class1 N=101 class0 N=0
PATHOLOGY M STAGE Kruskal-Wallis test N=14        
GENDER Wilcoxon test N=2 male N=2 female N=0
HISTOLOGICAL TYPE Kruskal-Wallis test N=206        
RADIATIONS RADIATION REGIMENINDICATION Wilcoxon test N=26 yes N=26 no N=0
RADIATIONEXPOSURE Wilcoxon test   N=0        
EXTRATHYROIDAL EXTENSION Kruskal-Wallis test N=80        
COMPLETENESS OF RESECTION Kruskal-Wallis test N=3        
NUMBER OF LYMPH NODES Spearman correlation test N=69 higher number.of.lymph.nodes N=43 lower number.of.lymph.nodes N=26
MULTIFOCALITY Wilcoxon test N=1 unifocal N=1 multifocal N=0
TUMOR SIZE Spearman correlation test N=14 higher tumor.size N=5 lower tumor.size N=9
RACE Kruskal-Wallis test N=6        
ETHNICITY Wilcoxon test N=5 not hispanic or latino N=5 hispanic or latino N=0
Clinical variable #1: 'Time to Death'

13 miRs related to 'Time to Death'.

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

Time to Death Duration (Months) 0-158.8 (median=16.6)
  censored N = 478
  death N = 14
     
  Significant markers N = 13
  associated with shorter survival 9
  associated with longer survival 4
List of top 10 miRs differentially expressed by 'Time to Death'

Table S2.  Get Full Table List of top 10 miRs significantly associated with 'Time to Death' by Cox regression test

HazardRatio Wald_P Q C_index
HSA-MIR-376A-1 4.3 1.852e-05 0.0095 0.884
HSA-MIR-181A-2 0.32 3.562e-05 0.018 0.175
HSA-MIR-487A 2.6 4.742e-05 0.024 0.844
HSA-MIR-425 5.4 4.898e-05 0.025 0.793
HSA-MIR-30D 0.14 7.536e-05 0.038 0.158
HSA-MIR-377 2.2 8.749e-05 0.044 0.834
HSA-MIR-496 2.2 0.0001625 0.082 0.844
HSA-MIR-181B-2 0.43 0.0001797 0.091 0.194
HSA-MIR-181B-1 0.36 0.0002347 0.12 0.226
HSA-MIR-206 1.44 0.0002595 0.13 0.807
Clinical variable #2: 'AGE'

18 miRs related to 'AGE'.

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

AGE Mean (SD) 47.18 (16)
  Significant markers N = 18
  pos. correlated 9
  neg. correlated 9
List of top 10 miRs differentially expressed by 'AGE'

Table S4.  Get Full Table List of top 10 miRs significantly correlated to 'AGE' by Spearman correlation test

SpearmanCorr corrP Q
HSA-MIR-625 -0.197 9.834e-06 0.00504
HSA-MIR-181A-2 -0.1917 1.715e-05 0.00876
HSA-MIR-376A-1 0.2526 1.821e-05 0.00929
HSA-MIR-3622A -0.1957 6.25e-05 0.0318
HSA-MIR-362 0.1761 8.037e-05 0.0408
HSA-MIR-181B-1 -0.1706 0.0001349 0.0684
HSA-MIR-1229 0.1873 0.0001444 0.073
HSA-MIR-539 0.1791 0.0001616 0.0816
HSA-MIR-196A-1 0.1779 0.0002166 0.109
HSA-MIR-629 -0.1618 0.0002959 0.149
Clinical variable #3: 'NEOPLASM.DISEASESTAGE'

54 miRs related to 'NEOPLASM.DISEASESTAGE'.

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

NEOPLASM.DISEASESTAGE Labels N
  STAGE I 280
  STAGE II 52
  STAGE III 109
  STAGE IV 2
  STAGE IVA 45
  STAGE IVC 6
     
  Significant markers N = 54
List of top 10 miRs differentially expressed by 'NEOPLASM.DISEASESTAGE'

Table S6.  Get Full Table List of top 10 miRs differentially expressed by 'NEOPLASM.DISEASESTAGE'

ANOVA_P Q
HSA-MIR-139 2.876e-08 1.47e-05
HSA-MIR-376C 9.78e-07 5e-04
HSA-MIR-126 1.021e-06 0.000521
HSA-MIR-154 1.167e-06 0.000594
HSA-MIR-199A-1 1.338e-06 0.00068
HSA-MIR-199A-2 1.908e-06 0.000967
HSA-MIR-214 2.128e-06 0.00108
HSA-MIR-199B 3.728e-06 0.00188
HSA-MIR-935 3.786e-06 0.00191
HSA-MIR-369 4.942e-06 0.00249
Clinical variable #4: 'PATHOLOGY.T.STAGE'

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

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

PATHOLOGY.T.STAGE Mean (SD) 2.13 (0.88)
  N
  1 141
  2 167
  3 164
  4 21
     
  Significant markers N = 39
  pos. correlated 19
  neg. correlated 20
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-139 -0.2666 1.825e-09 9.34e-07
HSA-MIR-126 -0.2567 7.389e-09 3.78e-06
HSA-MIR-363 -0.235 1.336e-07 6.82e-05
HSA-MIR-3074 -0.1978 9.618e-06 0.0049
HSA-MIR-7-2 -0.1978 1.243e-05 0.00631
HSA-MIR-145 -0.193 1.595e-05 0.00809
HSA-MIR-30C-2 -0.1911 1.946e-05 0.00985
HSA-MIR-92B 0.1887 2.487e-05 0.0126
HSA-MIR-20B -0.1888 2.492e-05 0.0126
HSA-MIR-129-1 0.1963 3.045e-05 0.0153
Clinical variable #5: 'PATHOLOGY.N.STAGE'

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

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

PATHOLOGY.N.STAGE Labels N
  class0 225
  class1 221
     
  Significant markers N = 101
  Higher in class1 101
  Higher in class0 0
List of top 10 miRs differentially expressed by 'PATHOLOGY.N.STAGE'

Table S10.  Get Full Table List of top 10 miRs differentially expressed by 'PATHOLOGY.N.STAGE'

W(pos if higher in 'class1') wilcoxontestP Q AUC
HSA-MIR-21 33711 7.967e-11 4.08e-08 0.6779
HSA-MIR-7-2 15101 1.087e-10 5.55e-08 0.6791
HSA-MIR-204 16311 3.321e-10 1.69e-07 0.672
HSA-MIR-1179 13653 4.444e-10 2.26e-07 0.6778
HSA-MIR-146B 33300 5.674e-10 2.88e-07 0.6697
HSA-MIR-511-2 32956 1.468e-09 7.44e-07 0.6657
HSA-MIR-3074 16842 3.796e-09 1.92e-06 0.6613
HSA-MIR-139 17094 1.145e-08 5.78e-06 0.6562
HSA-MIR-222 32451 2.469e-08 1.24e-05 0.6526
HSA-MIR-363 17370 5.273e-08 2.65e-05 0.6491
Clinical variable #6: 'PATHOLOGY.M.STAGE'

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

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

PATHOLOGY.M.STAGE Labels N
  M0 273
  M1 9
  MX 213
     
  Significant markers N = 14
List of top 10 miRs differentially expressed by 'PATHOLOGY.M.STAGE'

Table S12.  Get Full Table List of top 10 miRs differentially expressed by 'PATHOLOGY.M.STAGE'

ANOVA_P Q
HSA-MIR-3677 4.099e-06 0.0021
HSA-MIR-151 2.188e-05 0.0112
HSA-MIR-655 0.0001131 0.0577
HSA-MIR-136 0.0001207 0.0615
HSA-MIR-1274B 0.0001247 0.0633
HSA-MIR-3157 0.0002161 0.11
HSA-MIR-19B-1 0.0002205 0.112
HSA-MIR-589 0.0002307 0.117
HSA-MIR-331 0.0002375 0.12
HSA-MIR-3130-1 0.0002894 0.146
Clinical variable #7: 'GENDER'

2 miRs related to 'GENDER'.

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

GENDER Labels N
  FEMALE 364
  MALE 132
     
  Significant markers N = 2
  Higher in MALE 2
  Higher in FEMALE 0
List of 2 miRs differentially expressed by 'GENDER'

Table S14.  Get Full Table List of 2 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-651 16490 1.628e-07 8.34e-05 0.6539
HSA-MIR-361 18407 6.85e-05 0.035 0.6169
Clinical variable #8: 'HISTOLOGICAL.TYPE'

206 miRs related to 'HISTOLOGICAL.TYPE'.

Table S15.  Basic characteristics of clinical feature: 'HISTOLOGICAL.TYPE'

HISTOLOGICAL.TYPE Labels N
  OTHER SPECIFY 9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL 352
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED) 100
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES) 35
     
  Significant markers N = 206
List of top 10 miRs differentially expressed by 'HISTOLOGICAL.TYPE'

Table S16.  Get Full Table List of top 10 miRs differentially expressed by 'HISTOLOGICAL.TYPE'

ANOVA_P Q
HSA-MIR-21 1.831e-32 9.38e-30
HSA-MIR-7-2 7.127e-22 3.64e-19
HSA-MIR-146B 3.511e-21 1.79e-18
HSA-MIR-148B 4.957e-21 2.52e-18
HSA-MIR-511-2 5.458e-20 2.77e-17
HSA-MIR-511-1 1.43e-19 7.25e-17
HSA-MIR-30E 5.271e-19 2.67e-16
HSA-MIR-1179 8.815e-19 4.45e-16
HSA-MIR-204 1.163e-18 5.86e-16
HSA-MIR-1180 5.633e-18 2.83e-15
Clinical variable #9: 'RADIATIONS.RADIATION.REGIMENINDICATION'

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

Table S17.  Basic characteristics of clinical feature: 'RADIATIONS.RADIATION.REGIMENINDICATION'

RADIATIONS.RADIATION.REGIMENINDICATION Labels N
  NO 14
  YES 482
     
  Significant markers N = 26
  Higher in YES 26
  Higher in NO 0
List of top 10 miRs differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

Table S18.  Get Full Table List of top 10 miRs differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

W(pos if higher in 'YES') wilcoxontestP Q AUC
HSA-MIR-374A 553 9.544e-08 4.75e-05 0.918
HSA-MIR-660 5978 8.448e-07 0.00042 0.8859
HSA-MIR-130A 5745 7.326e-06 0.00363 0.8514
HSA-MIR-324 5705 1.042e-05 0.00516 0.8454
HSA-MIR-20B 5652 1.49e-05 0.00736 0.8393
HSA-MIR-1266 1090 1.564e-05 0.00771 0.8385
HSA-MIR-18A 5644 1.763e-05 0.00867 0.8364
HSA-MIR-99A 5640 1.824e-05 0.00896 0.8358
HSA-MIR-532 5596 2.644e-05 0.013 0.8293
HSA-MIR-887 5497 5.428e-05 0.0265 0.8163
Clinical variable #10: 'RADIATIONEXPOSURE'

No miR related to 'RADIATIONEXPOSURE'.

Table S19.  Basic characteristics of clinical feature: 'RADIATIONEXPOSURE'

RADIATIONEXPOSURE Labels N
  NO 417
  YES 17
     
  Significant markers N = 0
Clinical variable #11: 'EXTRATHYROIDAL.EXTENSION'

80 miRs related to 'EXTRATHYROIDAL.EXTENSION'.

Table S20.  Basic characteristics of clinical feature: 'EXTRATHYROIDAL.EXTENSION'

EXTRATHYROIDAL.EXTENSION Labels N
  MINIMAL (T3) 129
  MODERATE/ADVANCED (T4A) 16
  NONE 330
  VERY ADVANCED (T4B) 1
     
  Significant markers N = 80
List of top 10 miRs differentially expressed by 'EXTRATHYROIDAL.EXTENSION'

Table S21.  Get Full Table List of top 10 miRs differentially expressed by 'EXTRATHYROIDAL.EXTENSION'

ANOVA_P Q
HSA-MIR-148B 7.805e-10 4e-07
HSA-MIR-21 1.891e-09 9.66e-07
HSA-MIR-363 5.114e-09 2.61e-06
HSA-MIR-127 6.901e-09 3.51e-06
HSA-MIR-376C 1.607e-08 8.16e-06
HSA-MIR-493 1.749e-08 8.87e-06
HSA-MIR-126 2.012e-08 1.02e-05
HSA-MIR-1179 2.923e-08 1.48e-05
HSA-MIR-1180 2.984e-08 1.5e-05
HSA-MIR-758 3.356e-08 1.69e-05
Clinical variable #12: 'COMPLETENESS.OF.RESECTION'

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

Table S22.  Basic characteristics of clinical feature: 'COMPLETENESS.OF.RESECTION'

COMPLETENESS.OF.RESECTION Labels N
  R0 379
  R1 51
  R2 4
  RX 30
     
  Significant markers N = 3
List of 3 miRs differentially expressed by 'COMPLETENESS.OF.RESECTION'

Table S23.  Get Full Table List of 3 miRs differentially expressed by 'COMPLETENESS.OF.RESECTION'

ANOVA_P Q
HSA-MIR-139 3.455e-05 0.0177
HSA-MIR-196A-1 0.0003799 0.194
HSA-MIR-935 0.0004461 0.228
Clinical variable #13: 'NUMBER.OF.LYMPH.NODES'

69 miRs related to 'NUMBER.OF.LYMPH.NODES'.

Table S24.  Basic characteristics of clinical feature: 'NUMBER.OF.LYMPH.NODES'

NUMBER.OF.LYMPH.NODES Mean (SD) 3.55 (6.2)
  Significant markers N = 69
  pos. correlated 43
  neg. correlated 26
List of top 10 miRs differentially expressed by 'NUMBER.OF.LYMPH.NODES'

Table S25.  Get Full Table List of top 10 miRs significantly correlated to 'NUMBER.OF.LYMPH.NODES' by Spearman correlation test

SpearmanCorr corrP Q
HSA-MIR-7-2 -0.2976 3.454e-09 1.77e-06
HSA-MIR-21 0.2698 6.027e-08 3.08e-05
HSA-MIR-1179 -0.2771 8.316e-08 4.24e-05
HSA-MIR-511-2 0.2664 9.227e-08 4.7e-05
HSA-MIR-382 0.273 9.536e-08 4.84e-05
HSA-MIR-30E -0.2617 1.518e-07 7.7e-05
HSA-MIR-874 -0.2612 1.613e-07 8.16e-05
HSA-MIR-199A-1 0.2611 1.622e-07 8.19e-05
HSA-MIR-134 0.2603 1.916e-07 9.65e-05
HSA-MIR-3074 -0.2594 1.969e-07 9.9e-05
Clinical variable #14: 'MULTIFOCALITY'

One miR related to 'MULTIFOCALITY'.

Table S26.  Basic characteristics of clinical feature: 'MULTIFOCALITY'

MULTIFOCALITY Labels N
  MULTIFOCAL 224
  UNIFOCAL 262
     
  Significant markers N = 1
  Higher in UNIFOCAL 1
  Higher in MULTIFOCAL 0
List of one miR differentially expressed by 'MULTIFOCALITY'

Table S27.  Get Full Table List of one miR differentially expressed by 'MULTIFOCALITY'

W(pos if higher in 'UNIFOCAL') wilcoxontestP Q AUC
HSA-MIR-132 23245 7.763e-05 0.0397 0.6039
Clinical variable #15: 'TUMOR.SIZE'

14 miRs related to 'TUMOR.SIZE'.

Table S28.  Basic characteristics of clinical feature: 'TUMOR.SIZE'

TUMOR.SIZE Mean (SD) 2.97 (1.6)
  Significant markers N = 14
  pos. correlated 5
  neg. correlated 9
List of top 10 miRs differentially expressed by 'TUMOR.SIZE'

Table S29.  Get Full Table List of top 10 miRs significantly correlated to 'TUMOR.SIZE' by Spearman correlation test

SpearmanCorr corrP Q
HSA-MIR-9-2 -0.2079 2.967e-05 0.0152
HSA-MIR-9-1 -0.2025 4.799e-05 0.0245
HSA-MIR-107 0.2006 5.691e-05 0.029
HSA-MIR-183 0.1938 0.0001016 0.0517
HSA-MIR-199A-1 -0.1876 0.0001703 0.0865
HSA-MIR-182 0.1822 0.0002619 0.133
HSA-MIR-199A-2 -0.1803 0.0003053 0.154
HSA-MIR-96 0.1775 0.0003789 0.191
HSA-MIR-375 -0.1761 0.0004232 0.213
HSA-MIR-18B 0.2158 0.0004579 0.23
Clinical variable #16: 'RACE'

6 miRs related to 'RACE'.

Table S30.  Basic characteristics of clinical feature: 'RACE'

RACE Labels N
  AMERICAN INDIAN OR ALASKA NATIVE 1
  ASIAN 49
  BLACK OR AFRICAN AMERICAN 26
  WHITE 322
     
  Significant markers N = 6
List of 6 miRs differentially expressed by 'RACE'

Table S31.  Get Full Table List of 6 miRs differentially expressed by 'RACE'

ANOVA_P Q
HSA-MIR-3130-1 4.027e-14 2.06e-11
HSA-MIR-20A 0.0001831 0.0936
HSA-MIR-17 0.0001969 0.1
HSA-MIR-3917 0.0003022 0.154
HSA-MIR-338 0.0003364 0.171
HSA-MIR-3161 0.0003904 0.198
Clinical variable #17: 'ETHNICITY'

5 miRs related to 'ETHNICITY'.

Table S32.  Basic characteristics of clinical feature: 'ETHNICITY'

ETHNICITY Labels N
  HISPANIC OR LATINO 38
  NOT HISPANIC OR LATINO 350
     
  Significant markers N = 5
  Higher in NOT HISPANIC OR LATINO 5
  Higher in HISPANIC OR LATINO 0
List of 5 miRs differentially expressed by 'ETHNICITY'

Table S33.  Get Full Table List of 5 miRs differentially expressed by 'ETHNICITY'

W(pos if higher in 'NOT HISPANIC OR LATINO') wilcoxontestP Q AUC
HSA-MIR-153-1 c("7972", "5.488e-05") c("7972", "5.488e-05") 0.0281 0.7052
HSA-MIR-934 c("2196", "0.0001925") c("2196", "0.0001925") 0.0984 0.7084
HSA-MIR-34A c("4221", "0.0002169") c("4221", "0.0002169") 0.111 0.6826
HSA-MIR-652 c("4269", "0.0002885") c("4269", "0.0002885") 0.147 0.679
HSA-MIR-3690 c("2648", "0.0003753") c("2648", "0.0003753") 0.191 0.6924
Methods & Data
Input
  • Expresson data file = THCA-TP.miRseq_RPKM_log2.txt

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

  • Number of patients = 496

  • Number of miRs = 512

  • Number of clinical features = 17

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.

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)