Correlation between gene methylation status and clinical features
Pheochromocytoma and Paraganglioma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1X929QF
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/C1X929QF
Overview
Introduction

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

Summary

Testing the association between 16782 genes and 10 clinical features across 179 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 5 clinical features related to at least one genes.

  • 30 genes correlated to 'YEARS_TO_BIRTH'.

    • NHLRC1 ,  AGPAT9 ,  ZCWPW2 ,  RANBP17 ,  KIF15 ,  ...

  • 30 genes correlated to 'TUMOR_TISSUE_SITE'.

    • IL1RL2 ,  UNC5B ,  PROSAPIP1 ,  TCAP ,  RMI1 ,  ...

  • 22 genes correlated to 'GENDER'.

    • DKFZP434L187 ,  KIF4B ,  HAS3 ,  TLE1 ,  FRG1B ,  ...

  • 30 genes correlated to 'HISTOLOGICAL_TYPE'.

    • IL1RL2 ,  PROSAPIP1 ,  UNC5B ,  PNMT ,  RMI1 ,  ...

  • 4 genes correlated to 'RACE'.

    • DENND4C ,  DARC ,  FLJ10661 ,  CWF19L1

  • No genes correlated to 'DAYS_TO_DEATH_OR_LAST_FUP', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'NUMBER_OF_LYMPH_NODES', 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=9 younger N=21
TUMOR_TISSUE_SITE Wilcoxon test N=30 extra-adrenal site N=30 adrenal gland N=0
GENDER Wilcoxon test N=22 male N=22 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_OF_LYMPH_NODES Spearman correlation test   N=0        
RACE Kruskal-Wallis test N=4        
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) 0.1-316.7 (median=24.7)
  censored N = 172
  death N = 6
     
  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) 47.33 (15)
  Significant markers N = 30
  pos. correlated 9
  neg. correlated 21
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
NHLRC1 0.407 1.568e-08 0.000263
AGPAT9 -0.3872 8.579e-08 0.00072
ZCWPW2 -0.3793 1.634e-07 0.000914
RANBP17 0.3651 5.027e-07 0.00211
KIF15 0.3492 1.658e-06 0.00556
PAPSS2 -0.3415 2.901e-06 0.00651
FGFBP2 -0.3393 3.39e-06 0.00651
HTA -0.3373 3.9e-06 0.00651
RRAGD -0.3365 4.108e-06 0.00651
LOC91149 -0.336 4.259e-06 0.00651
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
  ADRENAL GLAND 147
  EXTRA-ADRENAL SITE 32
     
  Significant markers N = 30
  Higher in EXTRA-ADRENAL SITE 30
  Higher in ADRENAL GLAND 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 'EXTRA-ADRENAL SITE') wilcoxontestP Q AUC
IL1RL2 4301 2.211e-13 3.39e-09 0.9143
UNC5B 4260 6.92e-13 3.39e-09 0.9056
PROSAPIP1 4258 7.312e-13 3.39e-09 0.9052
TCAP 4237 1.299e-12 3.39e-09 0.9007
RMI1 4236 1.335e-12 3.39e-09 0.9005
HOMER1 4230 1.571e-12 3.39e-09 0.8992
KCNJ5 4230 1.571e-12 3.39e-09 0.8992
PNMT 4229 1.614e-12 3.39e-09 0.899
FAM181B 4206 3e-12 5.03e-09 0.8941
PEBP4 4206 3e-12 5.03e-09 0.8941
Clinical variable #4: 'GENDER'

22 genes related to 'GENDER'.

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

GENDER Labels N
  FEMALE 101
  MALE 78
     
  Significant markers N = 22
  Higher in MALE 22
  Higher in FEMALE 0
List of top 10 genes differentially expressed by 'GENDER'

Table S7.  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
DKFZP434L187 7019 3.297e-19 5.53e-15 0.891
KIF4B 1473 7.381e-13 6.19e-09 0.813
HAS3 6356 2.071e-12 1.16e-08 0.8068
TLE1 1720 1.092e-10 4.58e-07 0.7817
FRG1B 1776 3.159e-10 1.06e-06 0.7746
ANKRD20A4 5706 2.765e-07 0.000773 0.7243
USP2 2445 1.395e-05 0.0334 0.6896
LOC221710 5365 3.371e-05 0.0707 0.681
RWDD2B 2545 5.041e-05 0.094 0.6769
C3ORF64 2563 6.298e-05 0.103 0.6747
Clinical variable #5: 'RADIATION_THERAPY'

No gene related to 'RADIATION_THERAPY'.

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

RADIATION_THERAPY Labels N
  NO 172
  YES 5
     
  Significant markers N = 0
Clinical variable #6: 'KARNOFSKY_PERFORMANCE_SCORE'

No gene related to 'KARNOFSKY_PERFORMANCE_SCORE'.

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

KARNOFSKY_PERFORMANCE_SCORE Mean (SD) 96.77 (6.2)
  Score N
  70 1
  80 2
  90 13
  100 46
     
  Significant markers N = 0
Clinical variable #7: 'HISTOLOGICAL_TYPE'

30 genes related to 'HISTOLOGICAL_TYPE'.

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

HISTOLOGICAL_TYPE Labels N
  PARAGANGLIOMA 18
  PARAGANGLIOMA; EXTRA-ADRENAL PHEOCHROMOCYTOMA 13
  PHEOCHROMOCYTOMA 148
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'HISTOLOGICAL_TYPE'

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

kruskal_wallis_P Q
IL1RL2 5.852e-12 5.84e-08
PROSAPIP1 7.22e-12 5.84e-08
UNC5B 1.045e-11 5.84e-08
PNMT 1.733e-11 6.11e-08
RMI1 1.821e-11 6.11e-08
TCAP 3.118e-11 8.72e-08
HOMER1 5.297e-11 1.27e-07
KCNJ5 6.126e-11 1.29e-07
FAM181B 7.942e-11 1.48e-07
PEBP4 9.138e-11 1.53e-07
Clinical variable #8: 'NUMBER_OF_LYMPH_NODES'

No gene related to 'NUMBER_OF_LYMPH_NODES'.

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

NUMBER_OF_LYMPH_NODES Mean (SD) 0.86 (2.8)
  Value N
  0 16
  1 3
  2 1
  13 1
     
  Significant markers N = 0
Clinical variable #9: 'RACE'

4 genes related to 'RACE'.

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

RACE Labels N
  AMERICAN INDIAN OR ALASKA NATIVE 1
  ASIAN 6
  BLACK OR AFRICAN AMERICAN 20
  WHITE 148
     
  Significant markers N = 4
List of 4 genes differentially expressed by 'RACE'

Table S14.  Get Full Table List of 4 genes differentially expressed by 'RACE'

kruskal_wallis_P Q
DENND4C 1.856e-05 0.267
DARC 4.02e-05 0.267
FLJ10661 5.732e-05 0.267
CWF19L1 6.354e-05 0.267
Clinical variable #10: 'ETHNICITY'

No gene related to 'ETHNICITY'.

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

ETHNICITY Labels N
  HISPANIC OR LATINO 5
  NOT HISPANIC OR LATINO 138
     
  Significant markers N = 0
Methods & Data
Input

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

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

  • Number of patients = 179

  • Number of genes = 16782

  • Number of clinical features = 10

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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