Correlation between miRseq expression and clinical features
Thyroid Adenocarcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C12V2DZK
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/C12V2DZK
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 514 miRs and 17 clinical features across 487 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 ,  ...

  • 22 miRs correlated to 'AGE'.

    • HSA-MIR-181A-2 ,  HSA-MIR-376A-1 ,  HSA-MIR-625 ,  HSA-MIR-539 ,  HSA-MIR-181B-1 ,  ...

  • 63 miRs correlated to 'NEOPLASM.DISEASESTAGE'.

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

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

    • HSA-MIR-139 ,  HSA-MIR-126 ,  HSA-MIR-363 ,  HSA-MIR-3074 ,  HSA-MIR-30C-2 ,  ...

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

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

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

    • HSA-MIR-151 ,  HSA-MIR-3677 ,  HSA-MIR-1274B ,  HSA-MIR-589 ,  HSA-MIR-331 ,  ...

  • 2 miRs correlated to 'GENDER'.

    • HSA-MIR-651 ,  HSA-MIR-361

  • 208 miRs correlated to 'HISTOLOGICAL.TYPE'.

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

  • 85 miRs correlated to 'EXTRATHYROIDAL.EXTENSION'.

    • HSA-MIR-148B ,  HSA-MIR-21 ,  HSA-MIR-363 ,  HSA-MIR-127 ,  HSA-MIR-126 ,  ...

  • 1 miR correlated to 'COMPLETENESS.OF.RESECTION'.

    • HSA-MIR-139

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

    • HSA-MIR-7-2 ,  HSA-MIR-1179 ,  HSA-MIR-21 ,  HSA-MIR-511-2 ,  HSA-MIR-30E ,  ...

  • 1 miR correlated to 'MULTIFOCALITY'.

    • HSA-MIR-132

  • 11 miRs correlated to 'TUMOR.SIZE'.

    • HSA-MIR-9-2 ,  HSA-MIR-183 ,  HSA-MIR-9-1 ,  HSA-MIR-107 ,  HSA-MIR-182 ,  ...

  • 1 miR correlated to 'RACE'.

    • HSA-MIR-3130-1

  • 5 miRs correlated to 'ETHNICITY'.

    • HSA-MIR-153-1 ,  HSA-MIR-34A ,  HSA-MIR-934 ,  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=22 older N=15 younger N=7
NEOPLASM DISEASESTAGE Kruskal-Wallis test N=63        
PATHOLOGY T STAGE Spearman correlation test N=43 higher stage N=20 lower stage N=23
PATHOLOGY N STAGE Wilcoxon test N=104 class1 N=104 class0 N=0
PATHOLOGY M STAGE Kruskal-Wallis test N=12        
GENDER Wilcoxon test N=2 male N=2 female N=0
HISTOLOGICAL TYPE Kruskal-Wallis test N=208        
RADIATIONS RADIATION REGIMENINDICATION Wilcoxon test N=26 yes N=26 no N=0
RADIATIONEXPOSURE Wilcoxon test   N=0        
EXTRATHYROIDAL EXTENSION Kruskal-Wallis test N=85        
COMPLETENESS OF RESECTION Kruskal-Wallis test N=1        
NUMBER OF LYMPH NODES Spearman correlation test N=80 higher number.of.lymph.nodes N=47 lower number.of.lymph.nodes N=33
MULTIFOCALITY Wilcoxon test N=1 unifocal N=1 multifocal N=0
TUMOR SIZE Spearman correlation test N=11 higher tumor.size N=5 lower tumor.size N=6
RACE Kruskal-Wallis test N=1        
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=15.8)
  censored N = 469
  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 4.2 2.281e-05 0.012 0.885
HSA-MIR-181A-2 0.33 4.786e-05 0.025 0.177
HSA-MIR-487A 2.6 5.773e-05 0.03 0.842
HSA-MIR-425 5.3 5.923e-05 0.03 0.791
HSA-MIR-30D 0.15 0.0001139 0.058 0.161
HSA-MIR-377 2.2 0.0001329 0.068 0.833
HSA-MIR-496 2.2 0.0001842 0.094 0.843
HSA-MIR-181B-2 0.43 0.0002131 0.11 0.196
HSA-MIR-210 1.82 0.0003084 0.16 0.849
HSA-MIR-181B-1 0.36 0.0003273 0.17 0.228
Clinical variable #2: 'AGE'

22 miRs related to 'AGE'.

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

AGE Mean (SD) 47.26 (16)
  Significant markers N = 22
  pos. correlated 15
  neg. correlated 7
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-181A-2 -0.198 1.068e-05 0.00549
HSA-MIR-376A-1 0.2588 1.24e-05 0.00636
HSA-MIR-625 -0.1876 3.106e-05 0.0159
HSA-MIR-539 0.1936 5.207e-05 0.0266
HSA-MIR-181B-1 -0.1776 8.144e-05 0.0415
HSA-MIR-3622A -0.1914 0.000104 0.0529
HSA-MIR-1229 0.1883 0.0001512 0.0768
HSA-MIR-494 0.2251 0.0001623 0.0823
HSA-MIR-320A -0.1681 0.0001938 0.0981
HSA-MIR-377 0.1875 0.0002367 0.12
Clinical variable #3: 'NEOPLASM.DISEASESTAGE'

63 miRs related to 'NEOPLASM.DISEASESTAGE'.

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

NEOPLASM.DISEASESTAGE Labels N
  STAGE I 275
  STAGE II 51
  STAGE III 107
  STAGE IV 2
  STAGE IVA 44
  STAGE IVC 6
     
  Significant markers N = 63
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 1.302e-08 6.69e-06
HSA-MIR-376C 2.705e-07 0.000139
HSA-MIR-154 2.818e-07 0.000144
HSA-MIR-126 5.024e-07 0.000257
HSA-MIR-199A-1 5.528e-07 0.000282
HSA-MIR-199A-2 7.125e-07 0.000363
HSA-MIR-214 7.167e-07 0.000364
HSA-MIR-369 9.118e-07 0.000462
HSA-MIR-199B 1.274e-06 0.000645
HSA-MIR-487B 2.812e-06 0.00142
Clinical variable #4: 'PATHOLOGY.T.STAGE'

43 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
  1 140
  2 164
  3 160
  4 21
     
  Significant markers N = 43
  pos. correlated 20
  neg. correlated 23
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 -0.2859 1.41e-10 7.25e-08
HSA-MIR-126 -0.273 9.795e-10 5.02e-07
HSA-MIR-363 -0.2468 3.787e-08 1.94e-05
HSA-MIR-3074 -0.2069 4.34e-06 0.00222
HSA-MIR-30C-2 -0.2067 4.433e-06 0.00226
HSA-MIR-145 -0.2039 5.98e-06 0.00304
HSA-MIR-7-2 -0.2063 6.107e-06 0.0031
HSA-MIR-20B -0.203 6.723e-06 0.00341
HSA-MIR-92B 0.2028 6.773e-06 0.00343
HSA-MIR-338 -0.1971 1.223e-05 0.00618
Clinical variable #5: 'PATHOLOGY.N.STAGE'

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

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

PATHOLOGY.N.STAGE Labels N
  class0 222
  class1 218
     
  Significant markers N = 104
  Higher in class1 104
  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 33196 1.513e-11 7.78e-09 0.6859
HSA-MIR-7-2 14261 1.564e-11 8.03e-09 0.6884
HSA-MIR-1179 12841 5.973e-11 3.06e-08 0.6879
HSA-MIR-204 15512 7.381e-11 3.77e-08 0.6795
HSA-MIR-146B 32618 2.732e-10 1.39e-07 0.674
HSA-MIR-511-2 32415 3.753e-10 1.91e-07 0.6728
HSA-MIR-139 16132 1.468e-09 7.46e-07 0.6667
HSA-MIR-3074 16162 1.688e-09 8.56e-07 0.666
HSA-MIR-222 31776 1.332e-08 6.74e-06 0.6566
HSA-MIR-363 16618 1.902e-08 9.6e-06 0.6551
Clinical variable #6: 'PATHOLOGY.M.STAGE'

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

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

PATHOLOGY.M.STAGE Labels N
  M0 267
  M1 9
  MX 210
     
  Significant markers N = 12
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-151 8.36e-06 0.0043
HSA-MIR-3677 1.037e-05 0.00532
HSA-MIR-1274B 9.561e-05 0.049
HSA-MIR-589 0.0001149 0.0587
HSA-MIR-331 0.0001374 0.0701
HSA-MIR-655 0.0001392 0.0708
HSA-MIR-3157 0.0001661 0.0844
HSA-MIR-3130-1 0.0001797 0.0911
HSA-MIR-19B-1 0.0002058 0.104
HSA-MIR-34B 0.0002167 0.109
Clinical variable #7: 'GENDER'

2 miRs related to 'GENDER'.

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

GENDER Labels N
  FEMALE 357
  MALE 130
     
  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 15816 1.331e-07 6.84e-05 0.6563
HSA-MIR-361 17790 8.106e-05 0.0416 0.6167
Clinical variable #8: 'HISTOLOGICAL.TYPE'

208 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 344
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED) 99
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES) 35
     
  Significant markers N = 208
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 5.155e-32 2.65e-29
HSA-MIR-7-2 1.561e-21 8.01e-19
HSA-MIR-148B 6.848e-21 3.51e-18
HSA-MIR-146B 7.193e-21 3.68e-18
HSA-MIR-511-2 1.495e-19 7.62e-17
HSA-MIR-511-1 2.774e-19 1.41e-16
HSA-MIR-30E 1.243e-18 6.32e-16
HSA-MIR-1179 1.697e-18 8.6e-16
HSA-MIR-204 1.897e-18 9.6e-16
HSA-MIR-1180 8.137e-18 4.11e-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 473
     
  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 547 1.008e-07 5.04e-05 0.9174
HSA-MIR-660 5867 8.458e-07 0.000422 0.886
HSA-MIR-130A 5629 7.974e-06 0.00397 0.85
HSA-MIR-324 5593 1.1e-05 0.00547 0.8446
HSA-MIR-20B 5539 1.597e-05 0.00792 0.8382
HSA-MIR-1266 1075 1.648e-05 0.00816 0.8377
HSA-MIR-18A 5528 1.944e-05 0.0096 0.8348
HSA-MIR-99A 5526 1.978e-05 0.00975 0.8345
HSA-MIR-532 5487 2.762e-05 0.0136 0.8286
HSA-MIR-887 5382 6.027e-05 0.0296 0.8145
Clinical variable #10: 'RADIATIONEXPOSURE'

No miR related to 'RADIATIONEXPOSURE'.

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

RADIATIONEXPOSURE Labels N
  NO 409
  YES 17
     
  Significant markers N = 0
Clinical variable #11: 'EXTRATHYROIDAL.EXTENSION'

85 miRs related to 'EXTRATHYROIDAL.EXTENSION'.

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

EXTRATHYROIDAL.EXTENSION Labels N
  MINIMAL (T3) 127
  MODERATE/ADVANCED (T4A) 16
  NONE 325
  VERY ADVANCED (T4B) 1
     
  Significant markers N = 85
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 9.878e-11 5.08e-08
HSA-MIR-21 7.488e-10 3.84e-07
HSA-MIR-363 1.225e-09 6.27e-07
HSA-MIR-127 2.397e-09 1.23e-06
HSA-MIR-126 3.915e-09 2e-06
HSA-MIR-493 5.35e-09 2.72e-06
HSA-MIR-758 6.941e-09 3.53e-06
HSA-MIR-1179 7.659e-09 3.88e-06
HSA-MIR-376C 8.927e-09 4.52e-06
HSA-MIR-1180 1.504e-08 7.6e-06
Clinical variable #12: 'COMPLETENESS.OF.RESECTION'

One miR related to 'COMPLETENESS.OF.RESECTION'.

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

COMPLETENESS.OF.RESECTION Labels N
  R0 374
  R1 49
  R2 4
  RX 29
     
  Significant markers N = 1
List of one miR differentially expressed by 'COMPLETENESS.OF.RESECTION'

Table S23.  Get Full Table List of one miR differentially expressed by 'COMPLETENESS.OF.RESECTION'

ANOVA_P Q
HSA-MIR-139 3.608e-05 0.0185
Clinical variable #13: 'NUMBER.OF.LYMPH.NODES'

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

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

NUMBER.OF.LYMPH.NODES Mean (SD) 3.53 (6.2)
  Significant markers N = 80
  pos. correlated 47
  neg. correlated 33
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 -0.3207 2.148e-10 1.1e-07
HSA-MIR-1179 -0.3001 7.266e-09 3.73e-06
HSA-MIR-21 0.286 1.056e-08 5.41e-06
HSA-MIR-511-2 0.281 2.027e-08 1.04e-05
HSA-MIR-30E -0.2726 5.303e-08 2.7e-05
HSA-MIR-382 0.2799 5.374e-08 2.74e-05
HSA-MIR-199A-1 0.2707 6.571e-08 3.34e-05
HSA-MIR-874 -0.2706 6.619e-08 3.36e-05
HSA-MIR-31 0.2693 8.323e-08 4.21e-05
HSA-MIR-199A-2 0.2676 9.391e-08 4.74e-05
Clinical variable #14: 'MULTIFOCALITY'

One miR related to 'MULTIFOCALITY'.

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

MULTIFOCALITY Labels N
  MULTIFOCAL 219
  UNIFOCAL 258
     
  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 22145 4.707e-05 0.0242 0.6081
Clinical variable #15: 'TUMOR.SIZE'

11 miRs related to 'TUMOR.SIZE'.

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

TUMOR.SIZE Mean (SD) 2.96 (1.6)
  Significant markers N = 11
  pos. correlated 5
  neg. correlated 6
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 -0.1983 8.427e-05 0.0433
HSA-MIR-183 0.1965 9.739e-05 0.05
HSA-MIR-9-1 -0.1944 0.0001161 0.0595
HSA-MIR-107 0.1913 0.0001495 0.0764
HSA-MIR-182 0.1881 0.0001946 0.0992
HSA-MIR-18B 0.2273 0.0002665 0.136
HSA-MIR-199A-1 -0.18 0.0003657 0.186
HSA-MIR-653 -0.1785 0.0004111 0.208
HSA-MIR-96 0.1768 0.0004675 0.237
HSA-MIR-205 -0.1768 0.0004739 0.239
Clinical variable #16: 'RACE'

One miR 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 20
  WHITE 319
     
  Significant markers N = 1
List of one miR differentially expressed by 'RACE'

Table S31.  Get Full Table List of one miR differentially expressed by 'RACE'

ANOVA_P Q
HSA-MIR-3130-1 1.863e-13 9.58e-11
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 341
     
  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("7759", "6.056e-05") c("7759", "6.056e-05") 0.0311 0.7043
HSA-MIR-34A c("4079", "0.0001798") c("4079", "0.0001798") 0.0922 0.6852
HSA-MIR-934 c("2165", "0.0002027") c("2165", "0.0002027") 0.104 0.7078
HSA-MIR-652 c("4149", "0.0002763") c("4149", "0.0002763") 0.141 0.6798
HSA-MIR-3690 c("2569", "0.0003517") c("2569", "0.0003517") 0.179 0.6936
Methods & Data
Input

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

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

  • Number of patients = 487

  • Number of miRs = 514

  • 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)
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