Correlation between gene methylation status and clinical features
Colorectal Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1DB816C
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/C1DB816C
Overview
Introduction

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

Summary

Testing the association between 16791 genes and 13 clinical features across 391 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 10 clinical features related to at least one genes.

  • 30 genes correlated to 'YEARS_TO_BIRTH'.

    • GDNF ,  KLF14 ,  PENK ,  ELOVL2 ,  CBS ,  ...

  • 30 genes correlated to 'TUMOR_TISSUE_SITE'.

    • PAPLN ,  SMPD1 ,  FAM13C ,  METTL3 ,  KLF3 ,  ...

  • 25 genes correlated to 'PATHOLOGIC_STAGE'.

    • UBE2L6 ,  APOL1 ,  CASP1 ,  C8ORF80 ,  FAS ,  ...

  • 6 genes correlated to 'PATHOLOGY_T_STAGE'.

    • PHYHIP ,  TIMP4 ,  TNS4 ,  EPHA2 ,  APOBEC4 ,  ...

  • 30 genes correlated to 'PATHOLOGY_N_STAGE'.

    • CASP1 ,  UBE2L6 ,  APOL1 ,  SP140L ,  IL12RB1 ,  ...

  • 30 genes correlated to 'PATHOLOGY_M_STAGE'.

    • UBE2L6 ,  EBF1 ,  PLAT ,  PSORS1C1 ,  RAB5A ,  ...

  • 30 genes correlated to 'GENDER'.

    • KIF4B ,  GPX1 ,  TUBB4 ,  PAFAH1B2 ,  MDH1B ,  ...

  • 30 genes correlated to 'HISTOLOGICAL_TYPE'.

    • PAPLN ,  SMPD1 ,  FAM13C ,  C20ORF43 ,  FOXC1 ,  ...

  • 30 genes correlated to 'RESIDUAL_TUMOR'.

    • TRAPPC6A ,  FAM55D ,  RIPK2 ,  IFNG ,  SGSH ,  ...

  • 30 genes correlated to 'NUMBER_OF_LYMPH_NODES'.

    • CASP1 ,  UBE2L6 ,  IL12RB1 ,  APOL1 ,  FAS ,  ...

  • No genes correlated to 'DAYS_TO_DEATH_OR_LAST_FUP', 'RADIATION_THERAPY', 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
TUMOR_TISSUE_SITE Wilcoxon test N=30 rectum N=30 colon N=0
PATHOLOGIC_STAGE Kruskal-Wallis test N=25        
PATHOLOGY_T_STAGE Spearman correlation test N=6 higher stage N=2 lower stage N=4
PATHOLOGY_N_STAGE Spearman correlation test N=30 higher stage N=24 lower stage N=6
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        
HISTOLOGICAL_TYPE Kruskal-Wallis test N=30        
RESIDUAL_TUMOR Kruskal-Wallis test N=30        
NUMBER_OF_LYMPH_NODES Spearman correlation test N=30 higher number_of_lymph_nodes N=24 lower number_of_lymph_nodes N=6
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) 0.2-148 (median=22.4)
  censored N = 303
  death N = 87
     
  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) 64.39 (13)
  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
GDNF 0.2937 3.511e-09 4.66e-05
KLF14 0.2901 5.553e-09 4.66e-05
PENK 0.2798 1.988e-08 0.000111
ELOVL2 0.2765 2.963e-08 0.000124
CBS 0.2732 4.344e-08 0.000135
PPM1E 0.2723 4.874e-08 0.000135
IDO2 0.271 5.644e-08 0.000135
GPR1 0.2694 6.781e-08 0.00014
CORO6 0.2673 8.618e-08 0.00014
EBF4 0.2665 9.486e-08 0.00014
Clinical variable #3: 'TUMOR_TISSUE_SITE'

30 genes related to 'TUMOR_TISSUE_SITE'.

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

TUMOR_TISSUE_SITE Labels N
  COLON 293
  RECTUM 96
     
  Significant markers N = 30
  Higher in RECTUM 30
  Higher in COLON 0
List of top 10 genes differentially expressed by 'TUMOR_TISSUE_SITE'

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

W(pos if higher in 'RECTUM') wilcoxontestP Q AUC
PAPLN 3632 1.029e-27 1.73e-23 0.8709
SMPD1 3740 3.544e-27 2.98e-23 0.867
FAM13C 3818 8.587e-27 4.81e-23 0.8643
METTL3 23595 2.259e-24 9.48e-21 0.8477
KLF3 4378 4.065e-24 1.37e-20 0.8444
TEF 4487 1.296e-23 3.63e-20 0.8405
FOXC1 4497 1.769e-23 4.24e-20 0.8396
SLC44A1 4561 2.827e-23 5.67e-20 0.8378
PAK2 4568 3.042e-23 5.67e-20 0.8376
CCDC85A 4578 3.378e-23 5.67e-20 0.8372
Clinical variable #4: 'PATHOLOGIC_STAGE'

25 genes related to 'PATHOLOGIC_STAGE'.

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

PATHOLOGIC_STAGE Labels N
  STAGE I 54
  STAGE IA 1
  STAGE II 21
  STAGE IIA 113
  STAGE IIB 8
  STAGE IIC 2
  STAGE III 9
  STAGE IIIA 12
  STAGE IIIB 62
  STAGE IIIC 36
  STAGE IV 29
  STAGE IVA 23
  STAGE IVB 2
     
  Significant markers N = 25
List of top 10 genes differentially expressed by 'PATHOLOGIC_STAGE'

Table S7.  Get Full Table List of top 10 genes differentially expressed by 'PATHOLOGIC_STAGE'

kruskal_wallis_P Q
UBE2L6 3.239e-08 0.000544
APOL1 1.141e-06 0.00958
CASP1 5.093e-06 0.0281
C8ORF80 8.32e-06 0.0281
FAS 8.357e-06 0.0281
SP140L 1.187e-05 0.0332
GTPBP4 3.995e-05 0.0841
EBF1 4.007e-05 0.0841
CASP5 5.998e-05 0.112
WARS 8.713e-05 0.143
Clinical variable #5: 'PATHOLOGY_T_STAGE'

6 genes related to 'PATHOLOGY_T_STAGE'.

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

PATHOLOGY_T_STAGE Mean (SD) 2.93 (0.62)
  N
  T1 11
  T2 55
  T3 271
  T4 51
     
  Significant markers N = 6
  pos. correlated 2
  neg. correlated 4
List of 6 genes differentially expressed by 'PATHOLOGY_T_STAGE'

Table S9.  Get Full Table List of 6 genes significantly correlated to 'PATHOLOGY_T_STAGE' by Spearman correlation test

SpearmanCorr corrP Q
PHYHIP -0.2395 1.829e-06 0.0307
TIMP4 0.2261 6.852e-06 0.0575
TNS4 -0.208 3.629e-05 0.203
EPHA2 -0.1957 0.0001047 0.298
APOBEC4 0.1955 0.0001059 0.298
CIITA -0.1955 0.0001066 0.298
Clinical variable #6: 'PATHOLOGY_N_STAGE'

30 genes related to 'PATHOLOGY_N_STAGE'.

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

PATHOLOGY_N_STAGE Mean (SD) 0.63 (0.78)
  N
  N0 213
  N1 103
  N2 71
     
  Significant markers N = 30
  pos. correlated 24
  neg. correlated 6
List of top 10 genes differentially expressed by 'PATHOLOGY_N_STAGE'

Table S11.  Get Full Table List of top 10 genes significantly correlated to 'PATHOLOGY_N_STAGE' by Spearman correlation test

SpearmanCorr corrP Q
CASP1 0.3281 3.654e-11 6.14e-07
UBE2L6 0.3214 9.45e-11 7.93e-07
APOL1 0.2972 2.471e-09 1.38e-05
SP140L 0.2799 2.131e-08 7.8e-05
IL12RB1 0.2792 2.322e-08 7.8e-05
ASPHD2 0.2754 3.647e-08 9.09e-05
FAS 0.2751 3.79e-08 9.09e-05
UBA7 0.2701 6.795e-08 0.000143
CASP5 0.2677 8.941e-08 0.000167
MARCH8 0.2628 1.551e-07 0.00026
Clinical variable #7: 'PATHOLOGY_M_STAGE'

30 genes related to 'PATHOLOGY_M_STAGE'.

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

PATHOLOGY_M_STAGE Labels N
  class0 266
  class1 53
     
  Significant markers N = 30
  Higher in class1 30
  Higher in class0 0
List of top 10 genes differentially expressed by 'PATHOLOGY_M_STAGE'

Table S13.  Get Full Table List of top 10 genes differentially expressed by 'PATHOLOGY_M_STAGE'

W(pos if higher in 'class1') wilcoxontestP Q AUC
UBE2L6 10023 1.237e-06 0.0208 0.711
EBF1 4374 1.289e-05 0.0732 0.6897
PLAT 4401 1.575e-05 0.0732 0.6878
PSORS1C1 4441 2.112e-05 0.0732 0.685
RAB5A 9652 2.191e-05 0.0732 0.6846
TFAP2C 4488 2.967e-05 0.0732 0.6817
CASP1 9591 3.398e-05 0.0732 0.6803
SMAD4 9253 3.49e-05 0.0732 0.6818
RNF213 9538 4.937e-05 0.0758 0.6765
ARAP2 9514 5.834e-05 0.0758 0.6748
Clinical variable #8: 'GENDER'

30 genes related to 'GENDER'.

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

GENDER Labels N
  FEMALE 179
  MALE 212
     
  Significant markers N = 30
  Higher in MALE 30
  Higher in FEMALE 0
List of top 10 genes differentially expressed by 'GENDER'

Table S15.  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 6011 2.509e-31 2.47e-27 0.8416
GPX1 6026 2.938e-31 2.47e-27 0.8412
TUBB4 29109 8.836e-20 4.95e-16 0.7671
PAFAH1B2 10992 7.574e-13 3.18e-09 0.7103
MDH1B 12571 8.9e-09 2.99e-05 0.6687
ZNF839 12713 1.878e-08 5.25e-05 0.665
RWDD2B 12877 4.36e-08 0.000105 0.6607
WBP11P1 25025 5.501e-08 0.000115 0.6595
UGDH 13003 8.21e-08 0.000153 0.6573
DAZL 13192 2.073e-07 0.000318 0.6524
Clinical variable #9: 'RADIATION_THERAPY'

No gene related to 'RADIATION_THERAPY'.

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

RADIATION_THERAPY Labels N
  NO 318
  YES 16
     
  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
  COLON ADENOCARCINOMA 251
  COLON MUCINOUS ADENOCARCINOMA 39
  RECTAL ADENOCARCINOMA 90
  RECTAL MUCINOUS ADENOCARCINOMA 6
     
  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
PAPLN 2.197e-26 3.69e-22
SMPD1 6.217e-26 5.22e-22
FAM13C 3.273e-25 1.83e-21
C20ORF43 8.498e-25 3.57e-21
FOXC1 4.16e-23 1.4e-19
CCDC85A 7.153e-23 2e-19
KLF3 1.342e-22 3.22e-19
METTL3 1.758e-22 3.36e-19
TEF 1.801e-22 3.36e-19
CYP19A1 3.444e-22 5.78e-19
Clinical variable #11: 'RESIDUAL_TUMOR'

30 genes related to 'RESIDUAL_TUMOR'.

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

RESIDUAL_TUMOR Labels N
  R0 259
  R1 5
  R2 7
  RX 29
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'RESIDUAL_TUMOR'

Table S20.  Get Full Table List of top 10 genes differentially expressed by 'RESIDUAL_TUMOR'

kruskal_wallis_P Q
TRAPPC6A 1.481e-05 0.171
FAM55D 2.269e-05 0.171
RIPK2 5.985e-05 0.171
IFNG 7.883e-05 0.171
SGSH 8.239e-05 0.171
LOC100302650 8.287e-05 0.171
RPSAP58 9.811e-05 0.171
JAM2 0.0001002 0.171
FBXL8 0.0001158 0.171
PROCA1 0.0001172 0.171
Clinical variable #12: 'NUMBER_OF_LYMPH_NODES'

30 genes related to 'NUMBER_OF_LYMPH_NODES'.

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

NUMBER_OF_LYMPH_NODES Mean (SD) 2.27 (4.8)
  Significant markers N = 30
  pos. correlated 24
  neg. correlated 6
List of top 10 genes differentially expressed by 'NUMBER_OF_LYMPH_NODES'

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

SpearmanCorr corrP Q
CASP1 0.338 5.476e-11 9.19e-07
UBE2L6 0.3247 3.302e-10 2.77e-06
IL12RB1 0.2934 1.61e-08 9.01e-05
APOL1 0.29 2.391e-08 1e-04
FAS 0.2839 4.787e-08 0.000161
CASP5 0.2695 2.336e-07 0.000654
SP140L 0.268 2.742e-07 0.000658
AMOTL2 -0.2643 4.056e-07 0.000851
ASPHD2 0.2571 8.496e-07 0.00159
MARCH8 0.2498 1.763e-06 0.00272
Clinical variable #13: 'ETHNICITY'

No gene related to 'ETHNICITY'.

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

ETHNICITY Labels N
  HISPANIC OR LATINO 5
  NOT HISPANIC OR LATINO 338
     
  Significant markers N = 0
Methods & Data
Input

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

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

  • Number of patients = 391

  • Number of genes = 16791

  • Number of clinical features = 13

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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