Correlation between gene methylation status and clinical features
Thyroid Adenocarcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1WQ02X9
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between gene methylation status and clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1WQ02X9
Overview
Introduction

This pipeline uses various statistical tests to identify genes whose promoter methylation levels correlated to selected clinical features.

Summary

Testing the association between 19705 genes and 17 clinical features across 501 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 15 clinical features related to at least one genes.

  • 30 genes correlated to 'YEARS_TO_BIRTH'.

    • MGA ,  INA ,  NHLRC1 ,  RANBP17 ,  SYNGR3 ,  ...

  • 30 genes correlated to 'NEOPLASM_DISEASESTAGE'.

    • MGA ,  TBKBP1 ,  INA ,  IFT140 ,  TMEM204 ,  ...

  • 30 genes correlated to 'PATHOLOGY_T_STAGE'.

    • TBKBP1 ,  IFT140 ,  TMEM204 ,  GJD3 ,  PDGFB ,  ...

  • 30 genes correlated to 'PATHOLOGY_N_STAGE'.

    • ST6GALNAC5 ,  BMP1 ,  DAGLA ,  MET ,  CPNE1__1 ,  ...

  • 30 genes correlated to 'PATHOLOGY_M_STAGE'.

    • RBM18 ,  CEBPG ,  ZNF687 ,  SLC5A5 ,  FGF20 ,  ...

  • 30 genes correlated to 'GENDER'.

    • ALG11__2 ,  UTP14C__1 ,  ETF1 ,  KIF4B ,  FAM35A ,  ...

  • 30 genes correlated to 'HISTOLOGICAL_TYPE'.

    • LEPR ,  LEPROT ,  PON2 ,  GPR115 ,  XDH ,  ...

  • 30 genes correlated to 'RADIATIONS_RADIATION_REGIMENINDICATION'.

    • KLHDC1 ,  C1ORF77 ,  S100A13__1 ,  PPOX ,  ZNF782 ,  ...

  • 30 genes correlated to 'RADIATION_EXPOSURE'.

    • DSCR3 ,  DNAJB2 ,  TMEM183A ,  TMEM183B ,  ITGAV ,  ...

  • 30 genes correlated to 'EXTRATHYROIDAL_EXTENSION'.

    • NRCAM ,  TBKBP1 ,  PDGFB ,  SLC34A2 ,  IFT140 ,  ...

  • 30 genes correlated to 'COMPLETENESS_OF_RESECTION'.

    • SLC25A37 ,  NECAB2 ,  EGLN2 ,  KCNK3 ,  B3GNT5 ,  ...

  • 30 genes correlated to 'NUMBER_OF_LYMPH_NODES'.

    • MET ,  FUT2 ,  TMEM173 ,  DAGLA ,  MACF1 ,  ...

  • 4 genes correlated to 'MULTIFOCALITY'.

    • FTH1 ,  SORBS1 ,  SNF8 ,  BOC

  • 30 genes correlated to 'TUMOR_SIZE'.

    • TGFBR1 ,  KRTCAP3 ,  NRBP1 ,  ALDOC__1 ,  KCNQ4 ,  ...

  • 30 genes correlated to 'RACE'.

    • SCAMP5 ,  CDKN2AIP ,  RAD21L1 ,  EGOT ,  ITPR1 ,  ...

  • No genes correlated to 'DAYS_TO_DEATH_OR_LAST_FUP', and '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 genes that are significantly associated with each clinical feature at P value < 0.05 and Q value < 0.3.

Clinical feature Statistical test Significant genes Associated with                 Associated with
DAYS_TO_DEATH_OR_LAST_FUP Cox regression test   N=0        
YEARS_TO_BIRTH Spearman correlation test N=30 older N=30 younger N=0
NEOPLASM_DISEASESTAGE Kruskal-Wallis test N=30        
PATHOLOGY_T_STAGE Spearman correlation test N=30 higher stage N=22 lower stage N=8
PATHOLOGY_N_STAGE Wilcoxon test N=30 n1 N=30 n0 N=0
PATHOLOGY_M_STAGE Wilcoxon test N=30 class1 N=30 class0 N=0
GENDER Wilcoxon test N=30 male N=30 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=30 yes N=30 no N=0
EXTRATHYROIDAL_EXTENSION Kruskal-Wallis test N=30        
COMPLETENESS_OF_RESECTION Kruskal-Wallis test N=30        
NUMBER_OF_LYMPH_NODES Spearman correlation test N=30 higher number_of_lymph_nodes N=1 lower number_of_lymph_nodes N=29
MULTIFOCALITY Wilcoxon test N=4 unifocal N=4 multifocal N=0
TUMOR_SIZE Spearman correlation test N=30 higher tumor_size N=19 lower tumor_size N=11
RACE Kruskal-Wallis test N=30        
ETHNICITY Wilcoxon test   N=0        
Clinical variable #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

No gene 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=20.3)
  censored N = 486
  death N = 14
     
  Significant markers N = 0
Clinical variable #2: 'YEARS_TO_BIRTH'

30 genes related to 'YEARS_TO_BIRTH'.

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

YEARS_TO_BIRTH Mean (SD) 47.22 (16)
  Significant markers N = 30
  pos. correlated 30
  neg. correlated 0
List of top 10 genes differentially expressed by 'YEARS_TO_BIRTH'

Table S3.  Get Full Table List of top 10 genes significantly correlated to 'YEARS_TO_BIRTH' by Spearman correlation test

SpearmanCorr corrP Q
MGA 0.5334 3.525e-38 6.95e-34
INA 0.4904 1.139e-31 1.12e-27
NHLRC1 0.482 1.636e-30 1.07e-26
RANBP17 0.4699 6.887e-29 3.39e-25
SYNGR3 0.4685 1.076e-28 4.24e-25
C1ORF59 0.4661 2.213e-28 7.27e-25
ACN9 0.4543 6.911e-27 1.95e-23
OTUD7A 0.4502 2.263e-26 5.57e-23
ZNF518B 0.4403 3.611e-25 7.91e-22
NTNG2 0.429 7.633e-24 1.5e-20
Clinical variable #3: 'NEOPLASM_DISEASESTAGE'

30 genes related to 'NEOPLASM_DISEASESTAGE'.

Table S4.  Basic characteristics of clinical feature: 'NEOPLASM_DISEASESTAGE'

NEOPLASM_DISEASESTAGE Labels N
  STAGE I 283
  STAGE II 53
  STAGE III 109
  STAGE IV 2
  STAGE IVA 46
  STAGE IVC 6
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'NEOPLASM_DISEASESTAGE'

Table S5.  Get Full Table List of top 10 genes differentially expressed by 'NEOPLASM_DISEASESTAGE'

kruskal_wallis_P Q
MGA 2.884e-14 5.68e-10
TBKBP1 1.955e-13 1.93e-09
INA 9.055e-13 5.95e-09
IFT140 4.58e-12 1.81e-08
TMEM204 4.58e-12 1.81e-08
RANBP17 5.601e-12 1.84e-08
PDGFB 8.172e-11 2.09e-07
SPRY4 8.498e-11 2.09e-07
LOC728392 1.12e-10 2.45e-07
ZNF518B 1.33e-10 2.62e-07
Clinical variable #4: 'PATHOLOGY_T_STAGE'

30 genes related to 'PATHOLOGY_T_STAGE'.

Table S6.  Basic characteristics of clinical feature: 'PATHOLOGY_T_STAGE'

PATHOLOGY_T_STAGE Mean (SD) 2.14 (0.89)
  N
  T1 142
  T2 167
  T3 167
  T4 23
     
  Significant markers N = 30
  pos. correlated 22
  neg. correlated 8
List of top 10 genes differentially expressed by 'PATHOLOGY_T_STAGE'

Table S7.  Get Full Table List of top 10 genes significantly correlated to 'PATHOLOGY_T_STAGE' by Spearman correlation test

SpearmanCorr corrP Q
TBKBP1 0.3157 5.206e-13 1.03e-08
IFT140 0.3019 5.599e-12 2.82e-08
TMEM204 0.3019 5.599e-12 2.82e-08
GJD3 0.3018 5.73e-12 2.82e-08
PDGFB 0.2911 3.342e-11 1.32e-07
GGT7 0.2797 2.035e-10 6.68e-07
PSD3 -0.2761 3.518e-10 9.5e-07
FLJ42875 0.2755 3.858e-10 9.5e-07
PHLDA3 -0.2734 5.278e-10 1.16e-06
SCN4B 0.2698 8.975e-10 1.61e-06
Clinical variable #5: 'PATHOLOGY_N_STAGE'

30 genes related to 'PATHOLOGY_N_STAGE'.

Table S8.  Basic characteristics of clinical feature: 'PATHOLOGY_N_STAGE'

PATHOLOGY_N_STAGE Labels N
  N0 226
  N1 225
     
  Significant markers N = 30
  Higher in N1 30
  Higher in N0 0
List of top 10 genes differentially expressed by 'PATHOLOGY_N_STAGE'

Table S9.  Get Full Table List of top 10 genes differentially expressed by 'PATHOLOGY_N_STAGE'

W(pos if higher in 'N1') wilcoxontestP Q AUC
ST6GALNAC5 13220 1.16e-18 1.18e-14 0.74
BMP1 13288 1.796e-18 1.18e-14 0.7387
DAGLA 13288 1.796e-18 1.18e-14 0.7387
MET 13343 2.555e-18 1.26e-14 0.7376
CPNE1__1 13452 5.11e-18 1.49e-14 0.7355
RBM12__1 13452 5.11e-18 1.49e-14 0.7355
SLC34A2 13458 5.308e-18 1.49e-14 0.7353
PON2 13536 8.682e-18 2.14e-14 0.7338
CAPN2 13703 2.464e-17 5.39e-14 0.7305
MACF1 13727 2.859e-17 5.45e-14 0.73
Clinical variable #6: 'PATHOLOGY_M_STAGE'

30 genes related to 'PATHOLOGY_M_STAGE'.

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

PATHOLOGY_M_STAGE Labels N
  class0 278
  class1 9
     
  Significant markers N = 30
  Higher in class1 30
  Higher in class0 0
List of top 10 genes differentially expressed by 'PATHOLOGY_M_STAGE'

Table S11.  Get Full Table List of top 10 genes differentially expressed by 'PATHOLOGY_M_STAGE'

W(pos if higher in 'class1') wilcoxontestP Q AUC
RBM18 2229 6.634e-05 0.261 0.8909
CEBPG 2191 0.0001261 0.261 0.8757
ZNF687 311 0.0001261 0.261 0.8757
SLC5A5 2188 0.0001325 0.261 0.8745
FGF20 327 0.0001641 0.261 0.8693
GIPC2 2161 0.000206 0.261 0.8637
PFKFB4 341 0.000206 0.261 0.8637
CA14 358 0.0002704 0.261 0.8569
KRTCAP3__1 363 0.0002926 0.261 0.8549
MCOLN2 2139 0.0002926 0.261 0.8549
Clinical variable #7: 'GENDER'

30 genes related to 'GENDER'.

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

GENDER Labels N
  FEMALE 367
  MALE 134
     
  Significant markers N = 30
  Higher in MALE 30
  Higher in FEMALE 0
List of top 10 genes differentially expressed by 'GENDER'

Table S13.  Get Full Table List of top 10 genes 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
ALG11__2 48959 9.696e-65 9.55e-61 0.9955
UTP14C__1 48959 9.696e-65 9.55e-61 0.9955
ETF1 48487 2.51e-62 1.65e-58 0.9859
KIF4B 4877 5.631e-43 2.77e-39 0.9008
FAM35A 7877 2.264e-31 7.43e-28 0.8398
GLUD1__1 7877 2.264e-31 7.43e-28 0.8398
MTFR1 40985 2.933e-30 8.26e-27 0.8334
WBP11P1 39544 1.883e-25 4.64e-22 0.8041
ANKRD20A4 36376 2.078e-16 4.55e-13 0.7397
DACH1 13188 1.89e-15 3.72e-12 0.7318
Clinical variable #8: 'HISTOLOGICAL_TYPE'

30 genes 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 356
  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 genes differentially expressed by 'HISTOLOGICAL_TYPE'

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

kruskal_wallis_P Q
LEPR 2.949e-30 2.91e-26
LEPROT 2.949e-30 2.91e-26
PON2 8.631e-30 5.67e-26
GPR115 1.096e-28 5.4e-25
XDH 5.215e-28 2.06e-24
SLC34A2 6.622e-28 2.17e-24
MICAL2 1.389e-27 3.91e-24
CAPN2 1.858e-27 4.58e-24
SEC14L2 3.278e-27 6.59e-24
CD82 3.345e-27 6.59e-24
Clinical variable #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

30 genes related to 'RADIATIONS_RADIATION_REGIMENINDICATION'.

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

RADIATIONS_RADIATION_REGIMENINDICATION Labels N
  NO 14
  YES 487
     
  Significant markers N = 30
  Higher in YES 30
  Higher in NO 0
List of top 10 genes differentially expressed by 'RADIATIONS_RADIATION_REGIMENINDICATION'

Table S17.  Get Full Table List of top 10 genes differentially expressed by 'RADIATIONS_RADIATION_REGIMENINDICATION'

W(pos if higher in 'YES') wilcoxontestP Q AUC
KLHDC1 916 3.055e-06 0.0257 0.8656
C1ORF77 984 5.632e-06 0.0257 0.8557
S100A13__1 984 5.632e-06 0.0257 0.8557
PPOX 992 6.16e-06 0.0257 0.8542
ZNF782 1024 8.012e-06 0.0257 0.8498
COPS8 1030 8.443e-06 0.0257 0.8489
C13ORF23 1075 1.246e-05 0.0257 0.8423
NHLRC3 1075 1.246e-05 0.0257 0.8423
WBP4 1093 1.453e-05 0.0257 0.8397
WDR89 1103 1.582e-05 0.0257 0.8382
Clinical variable #10: 'RADIATION_EXPOSURE'

30 genes related to 'RADIATION_EXPOSURE'.

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

RADIATION_EXPOSURE Labels N
  NO 422
  YES 17
     
  Significant markers N = 30
  Higher in YES 30
  Higher in NO 0
List of top 10 genes differentially expressed by 'RADIATION_EXPOSURE'

Table S19.  Get Full Table List of top 10 genes differentially expressed by 'RADIATION_EXPOSURE'

W(pos if higher in 'YES') wilcoxontestP Q AUC
DSCR3 1490 4.357e-05 0.299 0.7923
DNAJB2 5583 9.993e-05 0.299 0.7782
TMEM183A 1605 0.0001118 0.299 0.7763
TMEM183B 1605 0.0001118 0.299 0.7763
ITGAV 5554 0.000126 0.299 0.7742
ROCK1 1622 0.000128 0.299 0.7739
SSX2IP 1656 0.0001672 0.299 0.7692
C5ORF41 1668 0.0001836 0.299 0.7675
ATM 1695 0.000226 0.299 0.7637
NPAT 1695 0.000226 0.299 0.7637
Clinical variable #11: 'EXTRATHYROIDAL_EXTENSION'

30 genes related to 'EXTRATHYROIDAL_EXTENSION'.

Table S20.  Basic characteristics of clinical feature: 'EXTRATHYROIDAL_EXTENSION'

EXTRATHYROIDAL_EXTENSION Labels N
  MINIMAL (T3) 132
  MODERATE/ADVANCED (T4A) 18
  NONE 332
  VERY ADVANCED (T4B) 1
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'EXTRATHYROIDAL_EXTENSION'

Table S21.  Get Full Table List of top 10 genes differentially expressed by 'EXTRATHYROIDAL_EXTENSION'

kruskal_wallis_P Q
NRCAM 1.396e-13 2.75e-09
TBKBP1 3.322e-13 3.27e-09
PDGFB 1.446e-12 9.5e-09
SLC34A2 3.369e-12 1.66e-08
IFT140 6.286e-12 2.06e-08
TMEM204 6.286e-12 2.06e-08
BBC3 7.419e-12 2.09e-08
GPR115 1.079e-11 2.66e-08
DUSP5 1.426e-11 3.07e-08
COL1A1 1.557e-11 3.07e-08
Clinical variable #12: 'COMPLETENESS_OF_RESECTION'

30 genes related to 'COMPLETENESS_OF_RESECTION'.

Table S22.  Basic characteristics of clinical feature: 'COMPLETENESS_OF_RESECTION'

COMPLETENESS_OF_RESECTION Labels N
  R0 383
  R1 52
  R2 4
  RX 30
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'COMPLETENESS_OF_RESECTION'

Table S23.  Get Full Table List of top 10 genes differentially expressed by 'COMPLETENESS_OF_RESECTION'

kruskal_wallis_P Q
SLC25A37 7.84e-06 0.0901
NECAB2 9.141e-06 0.0901
EGLN2 2.014e-05 0.101
KCNK3 2.324e-05 0.101
B3GNT5 3.159e-05 0.101
MCF2L2 3.159e-05 0.101
TTLL6 3.88e-05 0.101
TRIM3 4.448e-05 0.101
GALNTL2 4.629e-05 0.101
KATNAL1 8.063e-05 0.136
Clinical variable #13: 'NUMBER_OF_LYMPH_NODES'

30 genes related to 'NUMBER_OF_LYMPH_NODES'.

Table S24.  Basic characteristics of clinical feature: 'NUMBER_OF_LYMPH_NODES'

NUMBER_OF_LYMPH_NODES Mean (SD) 3.67 (6.2)
  Significant markers N = 30
  pos. correlated 1
  neg. correlated 29
List of top 10 genes differentially expressed by 'NUMBER_OF_LYMPH_NODES'

Table S25.  Get Full Table List of top 10 genes significantly correlated to 'NUMBER_OF_LYMPH_NODES' by Spearman correlation test

SpearmanCorr corrP Q
MET -0.4102 5.128e-17 1.01e-12
FUT2 -0.3976 5.438e-16 5.36e-12
TMEM173 -0.3953 8.154e-16 5.36e-12
DAGLA -0.3859 4.395e-15 2.16e-11
MACF1 -0.3837 6.431e-15 2.28e-11
TAGLN2 -0.3833 6.941e-15 2.28e-11
CAPN2 -0.3814 9.633e-15 2.52e-11
CPNE1__1 -0.3799 1.242e-14 2.52e-11
RBM12__1 -0.3799 1.242e-14 2.52e-11
SMURF1 -0.3798 1.278e-14 2.52e-11
Clinical variable #14: 'MULTIFOCALITY'

4 genes related to 'MULTIFOCALITY'.

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

MULTIFOCALITY Labels N
  MULTIFOCAL 226
  UNIFOCAL 265
     
  Significant markers N = 4
  Higher in UNIFOCAL 4
  Higher in MULTIFOCAL 0
List of 4 genes differentially expressed by 'MULTIFOCALITY'

Table S27.  Get Full Table List of 4 genes differentially expressed by 'MULTIFOCALITY'

W(pos if higher in 'UNIFOCAL') wilcoxontestP Q AUC
FTH1 23405 3.003e-05 0.26 0.6092
SORBS1 36369 4.145e-05 0.26 0.6073
SNF8 23597 5.106e-05 0.26 0.606
BOC 36281 5.275e-05 0.26 0.6058
Clinical variable #15: 'TUMOR_SIZE'

30 genes related to 'TUMOR_SIZE'.

Table S28.  Basic characteristics of clinical feature: 'TUMOR_SIZE'

TUMOR_SIZE Mean (SD) 2.98 (1.6)
  Significant markers N = 30
  pos. correlated 19
  neg. correlated 11
List of top 10 genes differentially expressed by 'TUMOR_SIZE'

Table S29.  Get Full Table List of top 10 genes significantly correlated to 'TUMOR_SIZE' by Spearman correlation test

SpearmanCorr corrP Q
TGFBR1 0.2294 3.349e-06 0.0364
KRTCAP3 0.2244 5.535e-06 0.0364
NRBP1 0.2244 5.535e-06 0.0364
ALDOC__1 0.2199 8.625e-06 0.0425
KCNQ4 0.2107 2.051e-05 0.0501
HOXD8 0.2101 2.161e-05 0.0501
UNKL 0.2098 2.226e-05 0.0501
MCOLN2 0.2096 2.266e-05 0.0501
FBXL21 0.209 2.404e-05 0.0501
DCI -0.208 2.636e-05 0.0501
Clinical variable #16: 'RACE'

30 genes related to 'RACE'.

Table S30.  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 genes differentially expressed by 'RACE'

Table S31.  Get Full Table List of top 10 genes differentially expressed by 'RACE'

kruskal_wallis_P Q
SCAMP5 4.241e-16 8.36e-12
CDKN2AIP 2.469e-11 2.43e-07
RAD21L1 1.035e-08 4e-05
EGOT 1.382e-08 4e-05
ITPR1 1.382e-08 4e-05
MRPS10 1.418e-08 4e-05
CLTC 1.574e-08 4e-05
PTGES 1.626e-08 4e-05
LOC253039 4.127e-08 8.13e-05
PSMD5 4.127e-08 8.13e-05
Clinical variable #17: 'ETHNICITY'

No gene related to 'ETHNICITY'.

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

ETHNICITY Labels N
  HISPANIC OR LATINO 38
  NOT HISPANIC OR LATINO 359
     
  Significant markers N = 0
Methods & Data
Input

  • Expresson data file = THCA-TP.meth.by_min_clin_corr.data.txt

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

  • Number of patients = 501

  • Number of genes = 19705

  • 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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