Correlation between gene methylation status and clinical features
Lung Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1PV6JS3
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between gene methylation status and clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1PV6JS3
Overview
Introduction

This pipeline uses various statistical tests to identify genes whose promoter methylation levels correlated to selected clinical features. The input file "LUAD-TP.meth.by_min_clin_corr.data.txt" is generated in the pipeline Methylation_Preprocess in stddata run.

Summary

Testing the association between 17084 genes and 15 clinical features across 458 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 11 clinical features related to at least one genes.

  • 30 genes correlated to 'DAYS_TO_DEATH_OR_LAST_FUP'.

    • PIK3R1 ,  ZFAND2A ,  KIAA1841 ,  CNR1 ,  GLO1 ,  ...

  • 30 genes correlated to 'YEARS_TO_BIRTH'.

    • MRPS33 ,  C14ORF169 ,  SNHG9 ,  KIF15 ,  ACN9 ,  ...

  • 30 genes correlated to 'PATHOLOGIC_STAGE'.

    • ENDOD1 ,  SEC11C ,  PLCB3 ,  ZFP112 ,  C11ORF41 ,  ...

  • 30 genes correlated to 'PATHOLOGY_T_STAGE'.

    • ACBD5 ,  IRF4 ,  SLC41A3 ,  NHEJ1 ,  DDX21 ,  ...

  • 30 genes correlated to 'PATHOLOGY_N_STAGE'.

    • GPRIN2 ,  DNAJC5 ,  C1ORF159 ,  SEC11C ,  EGLN2 ,  ...

  • 30 genes correlated to 'PATHOLOGY_M_STAGE'.

    • C6ORF136 ,  SLC38A3 ,  FAM64A ,  APLP1 ,  NOVA1 ,  ...

  • 30 genes correlated to 'GENDER'.

    • KIF4B ,  EIF4A1 ,  YARS2 ,  FRG1B ,  COX7C ,  ...

  • 30 genes correlated to 'HISTOLOGICAL_TYPE'.

    • LOC150622 ,  IQGAP1 ,  TRIM8 ,  ZMIZ1 ,  SEPW1 ,  ...

  • 30 genes correlated to 'NUMBER_PACK_YEARS_SMOKED'.

    • LOC150776 ,  DMGDH ,  PET112L ,  LILRB1 ,  CENPBD1 ,  ...

  • 30 genes correlated to 'YEAR_OF_TOBACCO_SMOKING_ONSET'.

    • C14ORF169 ,  MOGAT2 ,  MRPS33 ,  S100A16 ,  CALML4 ,  ...

  • 30 genes correlated to 'RACE'.

    • ZMYM1 ,  ATP6V1F ,  LOC100133161 ,  C14ORF167 ,  VPS35 ,  ...

  • No genes correlated to 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'RESIDUAL_TUMOR', 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=30   N=NA   N=NA
YEARS_TO_BIRTH Spearman correlation test N=30 older N=28 younger N=2
PATHOLOGIC_STAGE Kruskal-Wallis test N=30        
PATHOLOGY_T_STAGE Spearman correlation test N=30 higher stage N=7 lower stage N=23
PATHOLOGY_N_STAGE Spearman correlation test N=30 higher stage N=22 lower stage N=8
PATHOLOGY_M_STAGE Wilcoxon test N=30 class1 N=30 class0 N=0
GENDER Wilcoxon test N=30 male N=30 female N=0
RADIATION_THERAPY Wilcoxon test   N=0        
KARNOFSKY_PERFORMANCE_SCORE Spearman correlation test   N=0        
HISTOLOGICAL_TYPE Kruskal-Wallis test N=30        
NUMBER_PACK_YEARS_SMOKED Spearman correlation test N=30 higher number_pack_years_smoked N=5 lower number_pack_years_smoked N=25
YEAR_OF_TOBACCO_SMOKING_ONSET Spearman correlation test N=30 higher year_of_tobacco_smoking_onset N=24 lower year_of_tobacco_smoking_onset N=6
RESIDUAL_TUMOR Kruskal-Wallis test   N=0        
RACE Kruskal-Wallis test N=30        
ETHNICITY Wilcoxon test   N=0        
Clinical variable #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

30 genes 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) 0.1-238.3 (median=21.1)
  censored N = 292
  death N = 165
     
  Significant markers N = 30
  associated with shorter survival NA
  associated with longer survival NA
List of top 10 genes differentially expressed by 'DAYS_TO_DEATH_OR_LAST_FUP'

Table S2.  Get Full Table List of top 10 genes significantly associated with 'Time to Death' by Cox regression test. For the survival curves, it compared quantile intervals at c(0, 0.25, 0.50, 0.75, 1) and did not try survival analysis if there is only one interval.

logrank_P Q C_index
PIK3R1 1.47e-07 0.0015 0.614
ZFAND2A 1.73e-07 0.0015 0.38
KIAA1841 2.97e-07 0.0017 0.603
CNR1 8.88e-07 0.0038 0.595
GLO1 1.46e-06 0.0049 0.604
TMOD3 1.77e-06 0.0049 0.398
DDX11 2.01e-06 0.0049 0.442
CCDC13 2.75e-06 0.0059 0.623
WDR1 3.14e-06 0.006 0.405
ITPKB 3.75e-06 0.0064 0.606
Clinical variable #2: 'YEARS_TO_BIRTH'

30 genes related to 'YEARS_TO_BIRTH'.

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

YEARS_TO_BIRTH Mean (SD) 65.02 (10)
  Significant markers N = 30
  pos. correlated 28
  neg. correlated 2
List of top 10 genes differentially expressed by 'YEARS_TO_BIRTH'

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

SpearmanCorr corrP Q
MRPS33 0.4449 3.064e-22 5.23e-18
C14ORF169 0.3799 3.52e-16 3.01e-12
SNHG9 0.3622 9.67e-15 5.51e-11
KIF15 0.3338 1.272e-12 5.43e-09
ACN9 0.3127 3.664e-11 1.25e-07
FOXD2 0.2908 8.28e-10 2.36e-06
AARS2 0.282 2.776e-09 6.77e-06
BMP8A 0.2807 3.284e-09 7.01e-06
NHLRC1 0.2672 1.912e-08 3.63e-05
ZYG11A 0.2565 7.14e-08 0.000117
Clinical variable #3: 'PATHOLOGIC_STAGE'

30 genes related to 'PATHOLOGIC_STAGE'.

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

PATHOLOGIC_STAGE Labels N
  STAGE I 5
  STAGE IA 119
  STAGE IB 124
  STAGE II 1
  STAGE IIA 49
  STAGE IIB 62
  STAGE IIIA 64
  STAGE IIIB 9
  STAGE IV 20
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'PATHOLOGIC_STAGE'

Table S6.  Get Full Table List of top 10 genes differentially expressed by 'PATHOLOGIC_STAGE'

kruskal_wallis_P Q
ENDOD1 4.139e-06 0.041
SEC11C 4.801e-06 0.041
PLCB3 9.578e-06 0.0502
ZFP112 1.392e-05 0.0502
C11ORF41 1.49e-05 0.0502
PADI1 1.762e-05 0.0502
NOLC1 2.235e-05 0.0546
ST14 3.078e-05 0.0657
MOCOS 3.867e-05 0.0734
ARHGEF2 4.426e-05 0.0756
Clinical variable #4: 'PATHOLOGY_T_STAGE'

30 genes related to 'PATHOLOGY_T_STAGE'.

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

PATHOLOGY_T_STAGE Mean (SD) 1.82 (0.73)
  N
  T1 155
  T2 243
  T3 41
  T4 16
     
  Significant markers N = 30
  pos. correlated 7
  neg. correlated 23
List of top 10 genes differentially expressed by 'PATHOLOGY_T_STAGE'

Table S8.  Get Full Table List of top 10 genes significantly correlated to 'PATHOLOGY_T_STAGE' by Spearman correlation test

SpearmanCorr corrP Q
ACBD5 -0.2951 1.354e-10 2.31e-06
IRF4 0.2727 3.503e-09 2.99e-05
SLC41A3 -0.2669 7.367e-09 4.2e-05
NHEJ1 -0.2628 1.316e-08 5.62e-05
DDX21 -0.2543 3.787e-08 0.000117
NR1D2 -0.2527 4.655e-08 0.000117
NME2 -0.2524 4.808e-08 0.000117
PDE1C 0.2487 7.663e-08 0.000164
GLT1D1 0.2475 8.842e-08 0.000168
NUDT13 -0.2455 1.133e-07 0.000194
Clinical variable #5: 'PATHOLOGY_N_STAGE'

30 genes related to 'PATHOLOGY_N_STAGE'.

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

PATHOLOGY_N_STAGE Mean (SD) 0.48 (0.74)
  N
  N0 299
  N1 83
  N2 65
  N3 1
     
  Significant markers N = 30
  pos. correlated 22
  neg. correlated 8
List of top 10 genes differentially expressed by 'PATHOLOGY_N_STAGE'

Table S10.  Get Full Table List of top 10 genes significantly correlated to 'PATHOLOGY_N_STAGE' by Spearman correlation test

SpearmanCorr corrP Q
GPRIN2 0.2276 1.132e-06 0.0193
DNAJC5 0.2156 4.148e-06 0.0334
C1ORF159 0.2122 5.861e-06 0.0334
SEC11C 0.1946 3.377e-05 0.0846
EGLN2 0.1933 3.803e-05 0.0846
PLAGL2 0.193 3.906e-05 0.0846
GNB5 0.189 5.676e-05 0.0846
MYADM -0.1889 5.75e-05 0.0846
JOSD1 -0.1873 6.649e-05 0.0846
TMPRSS2 0.1871 6.737e-05 0.0846
Clinical variable #6: 'PATHOLOGY_M_STAGE'

30 genes related to 'PATHOLOGY_M_STAGE'.

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

PATHOLOGY_M_STAGE Labels N
  class0 295
  class1 19
     
  Significant markers N = 30
  Higher in class1 30
  Higher in class0 0
List of top 10 genes differentially expressed by 'PATHOLOGY_M_STAGE'

Table S12.  Get Full Table List of top 10 genes differentially expressed by 'PATHOLOGY_M_STAGE'

W(pos if higher in 'class1') wilcoxontestP Q AUC
C6ORF136 1119 1.146e-05 0.196 0.8004
SLC38A3 1240 4.657e-05 0.233 0.7788
FAM64A 1253 5.384e-05 0.233 0.7764
APLP1 1278 7.094e-05 0.233 0.772
NOVA1 1292 8.263e-05 0.233 0.7695
RALBP1 1293 8.354e-05 0.233 0.7693
SEC14L5 1324 0.0001166 0.233 0.7638
MRPL11 1345 0.0001456 0.233 0.76
PGBD4 1349 0.0001518 0.233 0.7593
ZNF530 1345 0.0001608 0.233 0.7584
Clinical variable #7: 'GENDER'

30 genes related to 'GENDER'.

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

GENDER Labels N
  FEMALE 244
  MALE 214
     
  Significant markers N = 30
  Higher in MALE 30
  Higher in FEMALE 0
List of top 10 genes differentially expressed by 'GENDER'

Table S14.  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
KIF4B 7760 1.537e-38 2.63e-34 0.8514
EIF4A1 11368 1.818e-25 1.55e-21 0.7823
YARS2 11641 1.363e-24 7.76e-21 0.7771
FRG1B 12191.5 7.073e-23 3.02e-19 0.7665
COX7C 13520 5.252e-19 1.79e-15 0.7411
RNASEH2C 37894 7.472e-17 2.13e-13 0.7257
RWDD2B 14670 5.818e-16 1.42e-12 0.7191
TBCA 15352 2.73e-14 5.83e-11 0.706
FUBP3 15629 1.221e-13 2.32e-10 0.7007
DDX43 15855 4.029e-13 6.88e-10 0.6964
Clinical variable #8: 'RADIATION_THERAPY'

No gene related to 'RADIATION_THERAPY'.

Table S15.  Basic characteristics of clinical feature: 'RADIATION_THERAPY'

RADIATION_THERAPY Labels N
  NO 377
  YES 55
     
  Significant markers N = 0
Clinical variable #9: 'KARNOFSKY_PERFORMANCE_SCORE'

No gene related to 'KARNOFSKY_PERFORMANCE_SCORE'.

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

KARNOFSKY_PERFORMANCE_SCORE Mean (SD) 79.76 (28)
  Significant markers N = 0
Clinical variable #10: 'HISTOLOGICAL_TYPE'

30 genes related to 'HISTOLOGICAL_TYPE'.

Table S17.  Basic characteristics of clinical feature: 'HISTOLOGICAL_TYPE'

HISTOLOGICAL_TYPE Labels N
  LUNG ACINAR ADENOCARCINOMA 18
  LUNG ADENOCARCINOMA MIXED SUBTYPE 92
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) 281
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS 5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS 19
  LUNG CLEAR CELL ADENOCARCINOMA 1
  LUNG MICROPAPILLARY ADENOCARCINOMA 2
  LUNG MUCINOUS ADENOCARCINOMA 2
  LUNG PAPILLARY ADENOCARCINOMA 22
  LUNG SIGNET RING ADENOCARCINOMA 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA 5
  MUCINOUS (COLLOID) CARCINOMA 10
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'HISTOLOGICAL_TYPE'

Table S18.  Get Full Table List of top 10 genes differentially expressed by 'HISTOLOGICAL_TYPE'

kruskal_wallis_P Q
LOC150622 4.398e-10 7.51e-06
IQGAP1 5.728e-07 0.00489
TRIM8 1.636e-06 0.00681
ZMIZ1 2.015e-06 0.00681
SEPW1 2.708e-06 0.00681
LIMD1 2.762e-06 0.00681
RLN3 2.791e-06 0.00681
SCMH1 4.523e-06 0.0087
KRT13 4.942e-06 0.0087
C10ORF105 5.134e-06 0.0087
Clinical variable #11: 'NUMBER_PACK_YEARS_SMOKED'

30 genes related to 'NUMBER_PACK_YEARS_SMOKED'.

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

NUMBER_PACK_YEARS_SMOKED Mean (SD) 40.94 (27)
  Significant markers N = 30
  pos. correlated 5
  neg. correlated 25
List of top 10 genes differentially expressed by 'NUMBER_PACK_YEARS_SMOKED'

Table S20.  Get Full Table List of top 10 genes significantly correlated to 'NUMBER_PACK_YEARS_SMOKED' by Spearman correlation test

SpearmanCorr corrP Q
LOC150776 -0.2827 3.821e-07 0.00653
DMGDH -0.251 7.223e-06 0.0617
PET112L -0.2382 2.114e-05 0.12
LILRB1 -0.227 5.189e-05 0.222
CENPBD1 -0.2203 8.686e-05 0.236
LRRTM4 -0.2181 0.0001032 0.236
GOT1 0.2162 0.0001183 0.236
H3F3B -0.2149 0.0001306 0.236
LOC284798 -0.2148 0.0001311 0.236
ZNF229 -0.2103 0.0001828 0.236
Clinical variable #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

30 genes related to 'YEAR_OF_TOBACCO_SMOKING_ONSET'.

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

YEAR_OF_TOBACCO_SMOKING_ONSET Mean (SD) 1965.3 (12)
  Significant markers N = 30
  pos. correlated 24
  neg. correlated 6
List of top 10 genes differentially expressed by 'YEAR_OF_TOBACCO_SMOKING_ONSET'

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

SpearmanCorr corrP Q
C14ORF169 -0.3101 5.117e-07 0.00588
MOGAT2 0.3067 6.888e-07 0.00588
MRPS33 -0.2987 1.369e-06 0.00779
S100A16 0.2719 1.199e-05 0.0357
CALML4 0.2713 1.261e-05 0.0357
BTBD17 0.2695 1.439e-05 0.0357
KBTBD2 -0.2693 1.461e-05 0.0357
PHKG1 0.2612 2.691e-05 0.0528
AATK 0.2596 3.024e-05 0.0528
ZNF362 0.2593 3.091e-05 0.0528
Clinical variable #13: 'RESIDUAL_TUMOR'

No gene related to 'RESIDUAL_TUMOR'.

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

RESIDUAL_TUMOR Labels N
  R0 295
  R1 11
  R2 1
  RX 23
     
  Significant markers N = 0
Clinical variable #14: 'RACE'

30 genes related to 'RACE'.

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

RACE Labels N
  ASIAN 6
  BLACK OR AFRICAN AMERICAN 50
  WHITE 353
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'RACE'

Table S25.  Get Full Table List of top 10 genes differentially expressed by 'RACE'

kruskal_wallis_P Q
ZMYM1 3.259e-13 5.57e-09
ATP6V1F 4.381e-11 3.74e-07
LOC100133161 1.711e-10 9.75e-07
C14ORF167 3.714e-10 1.34e-06
VPS35 3.923e-10 1.34e-06
GPBAR1 6.181e-10 1.69e-06
LOC147804 6.916e-10 1.69e-06
XPO7 8.542e-10 1.82e-06
RGPD5 1.089e-09 1.93e-06
LOC253039 1.132e-09 1.93e-06
Clinical variable #15: 'ETHNICITY'

No gene related to 'ETHNICITY'.

Table S26.  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.meth.by_min_clin_corr.data.txt

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

  • Number of patients = 458

  • Number of genes = 17084

  • Number of clinical features = 15

Selected clinical features

  • Further details on clinical features selected for this analysis, please find a documentation on selected CDEs (Clinical Data Elements). The first column of the file is a formula to convert values and the second column is a clinical parameter name.

  • 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, logrank test in univariate Cox regression analysis with proportional hazards model (Andersen and Gill 1982) was used to estimate the P values comparing quantile intervals using the 'coxph' function in R. Kaplan-Meier survival curves were plotted using quantile intervals at c(0, 0.25, 0.50, 0.75, 1). If there is only one interval group, it will not try survival analysis.

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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