Correlation between miRseq expression and clinical features
Thyroid Adenocarcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C147491D
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between miRseq expression and clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C147491D
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 500 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 15 clinical features related to at least one miRs.

  • 30 miRs correlated to 'DAYS_TO_DEATH_OR_LAST_FUP'.

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

  • 30 miRs correlated to 'YEARS_TO_BIRTH'.

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

  • 30 miRs correlated to 'NEOPLASM_DISEASESTAGE'.

    • HSA-MIR-139 ,  HSA-MIR-199A-1 ,  HSA-MIR-126 ,  HSA-MIR-376C ,  HSA-MIR-199A-2 ,  ...

  • 30 miRs correlated to 'PATHOLOGY_T_STAGE'.

    • HSA-MIR-139 ,  HSA-MIR-126 ,  HSA-MIR-363 ,  HSA-MIR-3074 ,  HSA-MIR-145 ,  ...

  • 30 miRs correlated to 'PATHOLOGY_N_STAGE'.

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

  • 2 miRs correlated to 'GENDER'.

    • HSA-MIR-651 ,  HSA-MIR-361

  • 30 miRs correlated to 'HISTOLOGICAL_TYPE'.

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

  • 30 miRs correlated to 'RADIATIONS_RADIATION_REGIMENINDICATION'.

    • HSA-MIR-374A ,  HSA-MIR-660 ,  HSA-MIR-130A ,  HSA-MIR-324 ,  HSA-MIR-1266 ,  ...

  • 30 miRs correlated to 'EXTRATHYROIDAL_EXTENSION'.

    • HSA-MIR-148B ,  HSA-MIR-21 ,  HSA-MIR-363 ,  HSA-MIR-127 ,  HSA-MIR-30E ,  ...

  • 3 miRs correlated to 'COMPLETENESS_OF_RESECTION'.

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

  • 30 miRs correlated to 'NUMBER_OF_LYMPH_NODES'.

    • HSA-MIR-7-2 ,  HSA-MIR-382 ,  HSA-MIR-199A-1 ,  HSA-MIR-1179 ,  HSA-MIR-222 ,  ...

  • 1 miR correlated to 'MULTIFOCALITY'.

    • HSA-MIR-132

  • 30 miRs correlated to 'TUMOR_SIZE'.

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

  • 30 miRs correlated to 'RACE'.

    • HSA-MIR-3130-1 ,  HSA-MIR-20A ,  HSA-MIR-17 ,  HSA-MIR-93 ,  HSA-MIR-3161 ,  ...

  • 21 miRs correlated to 'ETHNICITY'.

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

  • No miRs correlated to 'PATHOLOGY_M_STAGE', and 'RADIATION_EXPOSURE'.

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
DAYS_TO_DEATH_OR_LAST_FUP Cox regression test N=30 shorter survival N=24 longer survival N=6
YEARS_TO_BIRTH Spearman correlation test N=30 older N=16 younger N=14
NEOPLASM_DISEASESTAGE Kruskal-Wallis test N=30        
PATHOLOGY_T_STAGE Spearman correlation test N=30 higher stage N=9 lower stage N=21
PATHOLOGY_N_STAGE Wilcoxon test N=30 n1 N=30 n0 N=0
PATHOLOGY_M_STAGE Wilcoxon test   N=0        
GENDER Wilcoxon test N=2 male N=2 female N=0
HISTOLOGICAL_TYPE Kruskal-Wallis test N=30        
RADIATIONS_RADIATION_REGIMENINDICATION Wilcoxon test N=30 yes N=30 no N=0
RADIATION_EXPOSURE Wilcoxon test   N=0        
EXTRATHYROIDAL_EXTENSION Kruskal-Wallis test N=30        
COMPLETENESS_OF_RESECTION Kruskal-Wallis test N=3        
NUMBER_OF_LYMPH_NODES Spearman correlation test N=30 higher number_of_lymph_nodes N=21 lower number_of_lymph_nodes N=9
MULTIFOCALITY Wilcoxon test N=1 unifocal N=1 multifocal N=0
TUMOR_SIZE Spearman correlation test N=30 higher tumor_size N=10 lower tumor_size N=20
RACE Kruskal-Wallis test N=30        
ETHNICITY Wilcoxon test N=21 not hispanic or latino N=21 hispanic or latino N=0
Clinical variable #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

30 miRs related to 'DAYS_TO_DEATH_OR_LAST_FUP'.

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

DAYS_TO_DEATH_OR_LAST_FUP Duration (Months) 0.1-169.3 (median=20.4)
  censored N = 485
  death N = 14
     
  Significant markers N = 30
  associated with shorter survival 24
  associated with longer survival 6
List of top 10 miRs differentially expressed by 'DAYS_TO_DEATH_OR_LAST_FUP'

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 3.5 2.827e-05 0.011 0.879
HSA-MIR-181A-2 0.38 6.909e-05 0.011 0.182
HSA-MIR-487A 2.5 9.434e-05 0.011 0.826
HSA-MIR-425 4.9 9.73e-05 0.011 0.781
HSA-MIR-30D 0.19 0.0001117 0.011 0.162
HSA-MIR-377 2.2 0.0001393 0.011 0.831
HSA-MIR-496 2.3 0.0001568 0.011 0.84
HSA-MIR-299 2.1 0.0003599 0.022 0.828
HSA-MIR-181B-2 0.48 0.0003802 0.022 0.2
HSA-MIR-210 1.76 0.0005044 0.026 0.84
Clinical variable #2: 'YEARS_TO_BIRTH'

30 miRs related to 'YEARS_TO_BIRTH'.

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

YEARS_TO_BIRTH Mean (SD) 47.27 (16)
  Significant markers N = 30
  pos. correlated 16
  neg. correlated 14
List of top 10 miRs differentially expressed by 'YEARS_TO_BIRTH'

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

SpearmanCorr corrP Q
HSA-MIR-181A-2 -0.2012 5.814e-06 0.00153
HSA-MIR-376A-1 0.2629 6.839e-06 0.00153
HSA-MIR-625 -0.1972 8.95e-06 0.00153
HSA-MIR-181B-1 -0.1794 5.452e-05 0.00681
HSA-MIR-3622A -0.1942 6.715e-05 0.00681
HSA-MIR-196A-1 0.1886 7.997e-05 0.00681
HSA-MIR-539 0.1839 9.919e-05 0.00681
HSA-MIR-1229 0.1902 0.0001064 0.00681
HSA-MIR-362 0.1711 0.0001211 0.00689
HSA-MIR-424 -0.1653 0.0002043 0.00865
Clinical variable #3: 'NEOPLASM_DISEASESTAGE'

30 miRs related to 'NEOPLASM_DISEASESTAGE'.

Table S5.  Basic characteristics of clinical feature: 'NEOPLASM_DISEASESTAGE'

NEOPLASM_DISEASESTAGE Labels N
  STAGE I 282
  STAGE II 53
  STAGE III 109
  STAGE IV 2
  STAGE IVA 46
  STAGE IVC 6
     
  Significant markers N = 30
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'

kruskal_wallis_P Q
HSA-MIR-139 1.952e-08 9.99e-06
HSA-MIR-199A-1 4.21e-07 6.06e-05
HSA-MIR-126 4.309e-07 6.06e-05
HSA-MIR-376C 5.884e-07 6.06e-05
HSA-MIR-199A-2 5.916e-07 6.06e-05
HSA-MIR-214 7.713e-07 6.58e-05
HSA-MIR-199B 1.187e-06 8.05e-05
HSA-MIR-154 1.258e-06 8.05e-05
HSA-MIR-935 1.921e-06 0.000109
HSA-MIR-21 2.449e-06 0.000125
Clinical variable #4: 'PATHOLOGY_T_STAGE'

30 miRs related to 'PATHOLOGY_T_STAGE'.

Table S7.  Basic characteristics of clinical feature: 'PATHOLOGY_T_STAGE'

PATHOLOGY_T_STAGE Mean (SD) 2.14 (0.89)
  N
  T1 142
  T2 167
  T3 166
  T4 23
     
  Significant markers N = 30
  pos. correlated 9
  neg. correlated 21
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 -0.2697 9.489e-10 4.86e-07
HSA-MIR-126 -0.2591 4.431e-09 1.13e-06
HSA-MIR-363 -0.2361 1.005e-07 1.71e-05
HSA-MIR-3074 -0.2141 1.425e-06 0.000182
HSA-MIR-145 -0.196 1.058e-05 0.000982
HSA-MIR-7-2 -0.1966 1.326e-05 0.000982
HSA-MIR-433 0.2428 1.354e-05 0.000982
HSA-MIR-129-1 0.2015 1.649e-05 0.000982
HSA-MIR-30C-2 -0.1913 1.726e-05 0.000982
HSA-MIR-153-2 -0.189 2.192e-05 0.00109
Clinical variable #5: 'PATHOLOGY_N_STAGE'

30 miRs related to 'PATHOLOGY_N_STAGE'.

Table S9.  Basic characteristics of clinical feature: 'PATHOLOGY_N_STAGE'

PATHOLOGY_N_STAGE Labels N
  N0 226
  N1 224
     
  Significant markers N = 30
  Higher in N1 30
  Higher in N0 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 'N1') wilcoxontestP Q AUC
HSA-MIR-21 34296 7.375e-11 3.78e-08 0.6775
HSA-MIR-7-2 15387 2.044e-10 4.88e-08 0.6761
HSA-MIR-204 16613 2.859e-10 4.88e-08 0.6718
HSA-MIR-146B 33916 4.451e-10 5.7e-08 0.67
HSA-MIR-1179 13952 6.339e-10 6.49e-08 0.6755
HSA-MIR-511-2 33499 1.577e-09 1.35e-07 0.6647
HSA-MIR-3074 17165 3.505e-09 2.56e-07 0.6609
HSA-MIR-139 17484 1.389e-08 8.89e-07 0.6546
HSA-MIR-222 33091 1.708e-08 9.72e-07 0.6537
HSA-MIR-152 17807 5.31e-08 2.72e-06 0.6482
Clinical variable #6: 'PATHOLOGY_M_STAGE'

No miR related to 'PATHOLOGY_M_STAGE'.

Table S11.  Basic characteristics of clinical feature: 'PATHOLOGY_M_STAGE'

PATHOLOGY_M_STAGE Labels N
  class0 277
  class1 9
     
  Significant markers N = 0
Clinical variable #7: 'GENDER'

2 miRs related to 'GENDER'.

Table S12.  Basic characteristics of clinical feature: 'GENDER'

GENDER Labels N
  FEMALE 366
  MALE 134
     
  Significant markers N = 2
  Higher in MALE 2
  Higher in FEMALE 0
List of 2 miRs differentially expressed by 'GENDER'

Table S13.  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 16681 7.576e-08 3.88e-05 0.6571
HSA-MIR-361 18658 4.174e-05 0.0107 0.6196
Clinical variable #8: 'HISTOLOGICAL_TYPE'

30 miRs related to 'HISTOLOGICAL_TYPE'.

Table S14.  Basic characteristics of clinical feature: 'HISTOLOGICAL_TYPE'

HISTOLOGICAL_TYPE Labels N
  OTHER SPECIFY 9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL 355
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED) 100
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES) 36
     
  Significant markers N = 30
List of top 10 miRs differentially expressed by 'HISTOLOGICAL_TYPE'

Table S15.  Get Full Table List of top 10 miRs differentially expressed by 'HISTOLOGICAL_TYPE'

kruskal_wallis_P Q
HSA-MIR-21 8.413e-33 4.31e-30
HSA-MIR-7-2 5.606e-22 1.44e-19
HSA-MIR-146B 2.877e-21 4.91e-19
HSA-MIR-148B 4.169e-21 5.34e-19
HSA-MIR-511-2 1.685e-20 1.72e-18
HSA-MIR-511-1 4.324e-20 3.69e-18
HSA-MIR-30E 3.845e-19 2.81e-17
HSA-MIR-1179 6.037e-19 3.86e-17
HSA-MIR-204 8.58e-19 4.88e-17
HSA-MIR-1180 2.581e-18 1.32e-16
Clinical variable #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

30 miRs related to 'RADIATIONS_RADIATION_REGIMENINDICATION'.

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

RADIATIONS_RADIATION_REGIMENINDICATION Labels N
  NO 14
  YES 486
     
  Significant markers N = 30
  Higher in YES 30
  Higher in NO 0
List of top 10 miRs differentially expressed by 'RADIATIONS_RADIATION_REGIMENINDICATION'

Table S17.  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 9.067e-08 4.64e-05 0.9187
HSA-MIR-660 6030 8.23e-07 0.000211 0.8862
HSA-MIR-130A 5787 7.68e-06 0.00131 0.8505
HSA-MIR-324 5747 1.088e-05 0.00132 0.8447
HSA-MIR-1266 1095 1.508e-05 0.00132 0.8391
HSA-MIR-20B 5692 1.578e-05 0.00132 0.8383
HSA-MIR-18A 5688 1.802e-05 0.00132 0.836
HSA-MIR-99A 5671 2.079e-05 0.00133 0.8335
HSA-MIR-532 5640 2.692e-05 0.00153 0.8289
HSA-MIR-887 5550 5.109e-05 0.00258 0.8174
Clinical variable #10: 'RADIATION_EXPOSURE'

No miR related to 'RADIATION_EXPOSURE'.

Table S18.  Basic characteristics of clinical feature: 'RADIATION_EXPOSURE'

RADIATION_EXPOSURE Labels N
  NO 421
  YES 17
     
  Significant markers N = 0
Clinical variable #11: 'EXTRATHYROIDAL_EXTENSION'

30 miRs related to 'EXTRATHYROIDAL_EXTENSION'.

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

EXTRATHYROIDAL_EXTENSION Labels N
  MINIMAL (T3) 131
  MODERATE/ADVANCED (T4A) 18
  NONE 332
  VERY ADVANCED (T4B) 1
     
  Significant markers N = 30
List of top 10 miRs differentially expressed by 'EXTRATHYROIDAL_EXTENSION'

Table S20.  Get Full Table List of top 10 miRs differentially expressed by 'EXTRATHYROIDAL_EXTENSION'

kruskal_wallis_P Q
HSA-MIR-148B 1.444e-10 7.39e-08
HSA-MIR-21 4.772e-10 1.22e-07
HSA-MIR-363 2.396e-09 4.09e-07
HSA-MIR-127 3.898e-09 4.99e-07
HSA-MIR-30E 7.219e-09 6.21e-07
HSA-MIR-376C 7.279e-09 6.21e-07
HSA-MIR-493 9.63e-09 7.04e-07
HSA-MIR-1180 1.307e-08 8.36e-07
HSA-MIR-1179 1.717e-08 9.77e-07
HSA-MIR-126 2.255e-08 1.15e-06
Clinical variable #12: 'COMPLETENESS_OF_RESECTION'

3 miRs related to 'COMPLETENESS_OF_RESECTION'.

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

COMPLETENESS_OF_RESECTION Labels N
  R0 382
  R1 52
  R2 4
  RX 30
     
  Significant markers N = 3
List of 3 miRs differentially expressed by 'COMPLETENESS_OF_RESECTION'

Table S22.  Get Full Table List of 3 miRs differentially expressed by 'COMPLETENESS_OF_RESECTION'

kruskal_wallis_P Q
HSA-MIR-139 1.916e-05 0.00981
HSA-MIR-935 0.000271 0.0513
HSA-MIR-196A-1 0.0003006 0.0513
Clinical variable #13: 'NUMBER_OF_LYMPH_NODES'

30 miRs related to 'NUMBER_OF_LYMPH_NODES'.

Table S23.  Basic characteristics of clinical feature: 'NUMBER_OF_LYMPH_NODES'

NUMBER_OF_LYMPH_NODES Mean (SD) 3.66 (6.2)
  Significant markers N = 30
  pos. correlated 21
  neg. correlated 9
List of top 10 miRs differentially expressed by 'NUMBER_OF_LYMPH_NODES'

Table S24.  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 -0.2858 2.2e-08 1.13e-05
HSA-MIR-382 0.2675 2.045e-07 4.79e-05
HSA-MIR-199A-1 0.2521 5.764e-07 4.79e-05
HSA-MIR-1179 -0.2623 5.774e-07 4.79e-05
HSA-MIR-222 0.2497 7.433e-07 4.79e-05
HSA-MIR-199A-2 0.249 7.998e-07 4.79e-05
HSA-MIR-199B 0.2486 8.322e-07 4.79e-05
HSA-MIR-127 0.2477 9.152e-07 4.79e-05
HSA-MIR-21 0.2476 9.295e-07 4.79e-05
HSA-MIR-31 0.2472 1.004e-06 4.79e-05
Clinical variable #14: 'MULTIFOCALITY'

One miR related to 'MULTIFOCALITY'.

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

MULTIFOCALITY Labels N
  MULTIFOCAL 225
  UNIFOCAL 265
     
  Significant markers N = 1
  Higher in UNIFOCAL 1
  Higher in MULTIFOCAL 0
List of one miR differentially expressed by 'MULTIFOCALITY'

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

W(pos if higher in 'UNIFOCAL') wilcoxontestP Q AUC
HSA-MIR-132 23496 5.262e-05 0.0269 0.6059
Clinical variable #15: 'TUMOR_SIZE'

30 miRs related to 'TUMOR_SIZE'.

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

TUMOR_SIZE Mean (SD) 2.98 (1.6)
  Significant markers N = 30
  pos. correlated 10
  neg. correlated 20
List of top 10 miRs differentially expressed by 'TUMOR_SIZE'

Table S28.  Get Full Table List of top 10 miRs significantly correlated to 'TUMOR_SIZE' by Spearman correlation test

SpearmanCorr corrP Q
HSA-MIR-9-2 -0.212 1.862e-05 0.00784
HSA-MIR-9-1 -0.2066 3.063e-05 0.00784
HSA-MIR-183 0.1983 6.396e-05 0.0109
HSA-MIR-107 0.1879 0.000154 0.0133
HSA-MIR-182 0.1867 0.0001694 0.0133
HSA-MIR-199A-1 -0.1864 0.0001736 0.0133
HSA-MIR-153-2 -0.1859 0.0001816 0.0133
HSA-MIR-96 0.1821 0.0002462 0.0158
HSA-MIR-199A-2 -0.1792 0.0003102 0.0164
HSA-MIR-142 -0.1777 0.0003501 0.0164
Clinical variable #16: 'RACE'

30 miRs related to 'RACE'.

Table S29.  Basic characteristics of clinical feature: 'RACE'

RACE Labels N
  AMERICAN INDIAN OR ALASKA NATIVE 1
  ASIAN 52
  BLACK OR AFRICAN AMERICAN 27
  WHITE 326
     
  Significant markers N = 30
List of top 10 miRs differentially expressed by 'RACE'

Table S30.  Get Full Table List of top 10 miRs differentially expressed by 'RACE'

kruskal_wallis_P Q
HSA-MIR-3130-1 3.868e-15 1.98e-12
HSA-MIR-20A 8.898e-05 0.0228
HSA-MIR-17 0.0001553 0.0265
HSA-MIR-93 0.0003694 0.0355
HSA-MIR-3161 0.0004467 0.0355
HSA-MIR-338 0.0004552 0.0355
HSA-MIR-4326 0.0004856 0.0355
HSA-MIR-3917 0.0006246 0.04
HSA-MIR-548V 0.0008531 0.0405
HSA-MIR-1255A 0.0008554 0.0405
Clinical variable #17: 'ETHNICITY'

21 miRs related to 'ETHNICITY'.

Table S31.  Basic characteristics of clinical feature: 'ETHNICITY'

ETHNICITY Labels N
  HISPANIC OR LATINO 38
  NOT HISPANIC OR LATINO 358
     
  Significant markers N = 21
  Higher in NOT HISPANIC OR LATINO 21
  Higher in HISPANIC OR LATINO 0
Methods & Data
Input

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

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

  • Number of patients = 500

  • Number of miRs = 512

  • Number of clinical features = 17

Selected clinical features

  • For clinical features selected for this analysis and their value conozzle.versions, please find a documentation on selected CDEs .

  • Survival time data

    • Survival time data is a combined value of days_to_death and days_to_last_followup. For each patient, it creates a combined value 'days_to_death_or_last_fup' using conversion process below.

      • if 'vital_status'==1(dead), 'days_to_last_followup' is always NA. Thus, uses 'days_to_death' value for 'days_to_death_or_fup'

      • if 'vital_status'==0(alive),

        • if 'days_to_death'==NA & 'days_to_last_followup'!=NA, uses 'days_to_last_followup' value for 'days_to_death_or_fup'

        • if 'days_to_death'!=NA, excludes this case in survival analysis and report the case.

      • if 'vital_status'==NA,excludes this case in survival analysis and report the case.

    • cf. In certain diesase types such as SKCM, days_to_death parameter is replaced with time_from_specimen_dx or time_from_specimen_procurement_to_death .

  • This analysis excluded clinical variables that has only NA values.

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

Wilcoxon rank sum test (Mann-Whitney U test)

For two groups (mutant or wild-type) of continuous type of clinical data, wilcoxon rank sum test (Mann and Whitney, 1947) was applied to compare their mean difference using 'wilcox.test(continuous.clinical ~ as.factor(group), exact=FALSE)' function in R. This test is equivalent to the Mann-Whitney test.

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] Mann and Whitney, On a Test of Whether one of Two Random Variables is Stochastically Larger than the Other, Annals of Mathematical Statistics 18 (1), 50-60 (1947)
[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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