Correlation between gene methylation status and clinical features
Lung Adenocarcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C15T3HZS
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between gene methylation status and clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C15T3HZS
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 19992 genes and 13 clinical features across 396 samples, statistically thresholded by Q value < 0.05, 10 clinical features related to at least one genes.

  • 7 genes correlated to 'AGE'.

    • BMP8A ,  KIAA1143 ,  KIF15 ,  LOC148696 ,  CLEC5A ,  ...

  • 14 genes correlated to 'NEOPLASM.DISEASESTAGE'.

    • PAN2 ,  ZNF546 ,  MRPS14 ,  PRPF31 ,  TFPT ,  ...

  • 13 genes correlated to 'PATHOLOGY.T.STAGE'.

    • ACBD5 ,  TACC2 ,  PRDM15 ,  SLC41A3 ,  NME1-NME2 ,  ...

  • 2 genes correlated to 'PATHOLOGY.N.STAGE'.

    • POLR2J3__1 ,  VAMP1

  • 192 genes correlated to 'PATHOLOGY.M.STAGE'.

    • PPP2R5B ,  C8ORF55 ,  HOMER3 ,  KILLIN ,  PTEN ,  ...

  • 98 genes correlated to 'GENDER'.

    • KIF4B ,  EIF4A1 ,  SNORA48 ,  RNASEH2C ,  COX7C ,  ...

  • 102 genes correlated to 'HISTOLOGICAL.TYPE'.

    • DNAJC25-GNG10__1 ,  GNG10 ,  METTL2A ,  RAD9A ,  PDCD11 ,  ...

  • 64 genes correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

    • NT5E ,  KIAA1529 ,  GRIK4 ,  ZNF642 ,  GALNT14 ,  ...

  • 2 genes correlated to 'NUMBERPACKYEARSSMOKED'.

    • FAM128A__1 ,  LOC150776__1

  • 122 genes correlated to 'COMPLETENESS.OF.RESECTION'.

    • DDX52 ,  CCDC53 ,  ANKIB1 ,  KRIT1 ,  SLC6A16 ,  ...

  • No genes correlated to 'Time to Death', 'KARNOFSKY.PERFORMANCE.SCORE', and 'YEAROFTOBACCOSMOKINGONSET'.

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 Q value < 0.05.

Clinical feature Statistical test Significant genes Associated with                 Associated with
Time to Death Cox regression test   N=0        
AGE Spearman correlation test N=7 older N=6 younger N=1
NEOPLASM DISEASESTAGE ANOVA test N=14        
PATHOLOGY T STAGE Spearman correlation test N=13 higher stage N=5 lower stage N=8
PATHOLOGY N STAGE Spearman correlation test N=2 higher stage N=1 lower stage N=1
PATHOLOGY M STAGE ANOVA test N=192        
GENDER t test N=98 male N=10 female N=88
KARNOFSKY PERFORMANCE SCORE Spearman correlation test   N=0        
HISTOLOGICAL TYPE ANOVA test N=102        
RADIATIONS RADIATION REGIMENINDICATION t test N=64 yes N=47 no N=17
NUMBERPACKYEARSSMOKED Spearman correlation test N=2 higher numberpackyearssmoked N=0 lower numberpackyearssmoked N=2
YEAROFTOBACCOSMOKINGONSET Spearman correlation test   N=0        
COMPLETENESS OF RESECTION ANOVA test N=122        
Clinical variable #1: 'Time to Death'

No gene related to 'Time to Death'.

Table S1.  Basic characteristics of clinical feature: 'Time to Death'

Time to Death Duration (Months) 0-224 (median=10.9)
  censored N = 265
  death N = 98
     
  Significant markers N = 0
Clinical variable #2: 'AGE'

7 genes related to 'AGE'.

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

AGE Mean (SD) 65.2 (10)
  Significant markers N = 7
  pos. correlated 6
  neg. correlated 1
List of 7 genes significantly correlated to 'AGE' by Spearman correlation test

Table S3.  Get Full Table List of 7 genes significantly correlated to 'AGE' by Spearman correlation test

SpearmanCorr corrP Q
BMP8A 0.2727 1.064e-07 0.00213
KIAA1143 0.2669 2.034e-07 0.00407
KIF15 0.2669 2.034e-07 0.00407
LOC148696 -0.2632 3.002e-07 0.006
CLEC5A 0.2616 3.595e-07 0.00719
NHLRC1 0.2501 1.175e-06 0.0235
B4GALNT4 0.2459 1.792e-06 0.0358

Figure S1.  Get High-res Image As an example, this figure shows the association of BMP8A to 'AGE'. P value = 1.06e-07 with Spearman correlation analysis. The straight line presents the best linear regression.

Clinical variable #3: 'NEOPLASM.DISEASESTAGE'

14 genes related to 'NEOPLASM.DISEASESTAGE'.

Table S4.  Basic characteristics of clinical feature: 'NEOPLASM.DISEASESTAGE'

NEOPLASM.DISEASESTAGE Labels N
  STAGE I 3
  STAGE IA 98
  STAGE IB 115
  STAGE IIA 41
  STAGE IIB 55
  STAGE IIIA 57
  STAGE IIIB 9
  STAGE IV 17
     
  Significant markers N = 14
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'

ANOVA_P Q
PAN2 2.134e-12 4.27e-08
ZNF546 1.24e-10 2.48e-06
MRPS14 4.534e-10 9.06e-06
PRPF31 9.57e-10 1.91e-05
TFPT 9.57e-10 1.91e-05
ASNA1 3.282e-09 6.56e-05
PAFAH1B3__1 6.557e-08 0.00131
PRR19__1 6.557e-08 0.00131
RNF187 1.498e-07 0.00299
TMED2 3.807e-07 0.00761

Figure S2.  Get High-res Image As an example, this figure shows the association of PAN2 to 'NEOPLASM.DISEASESTAGE'. P value = 2.13e-12 with ANOVA analysis.

Clinical variable #4: 'PATHOLOGY.T.STAGE'

13 genes related to 'PATHOLOGY.T.STAGE'.

Table S6.  Basic characteristics of clinical feature: 'PATHOLOGY.T.STAGE'

PATHOLOGY.T.STAGE Mean (SD) 1.84 (0.73)
  N
  1 125
  2 219
  3 34
  4 15
     
  Significant markers N = 13
  pos. correlated 5
  neg. correlated 8
List of top 10 genes significantly correlated to 'PATHOLOGY.T.STAGE' by Spearman correlation test

Table S7.  Get Full Table List of top 10 genes significantly correlated to 'PATHOLOGY.T.STAGE' by Spearman correlation test

SpearmanCorr corrP Q
ACBD5 -0.278 2.084e-08 0.000417
TACC2 -0.262 1.362e-07 0.00272
PRDM15 0.2594 1.826e-07 0.00365
SLC41A3 -0.2477 6.578e-07 0.0131
NME1-NME2 -0.2474 6.813e-07 0.0136
NME2 -0.2474 6.813e-07 0.0136
DDX21 -0.2441 9.721e-07 0.0194
GLT1D1 0.2391 1.63e-06 0.0326
HDAC7 0.2371 1.999e-06 0.04
PDE1C 0.2367 2.083e-06 0.0416

Figure S3.  Get High-res Image As an example, this figure shows the association of ACBD5 to 'PATHOLOGY.T.STAGE'. P value = 2.08e-08 with Spearman correlation analysis.

Clinical variable #5: 'PATHOLOGY.N.STAGE'

2 genes related to 'PATHOLOGY.N.STAGE'.

Table S8.  Basic characteristics of clinical feature: 'PATHOLOGY.N.STAGE'

PATHOLOGY.N.STAGE Mean (SD) 0.5 (0.76)
  N
  0 255
  1 72
  2 59
  3 1
     
  Significant markers N = 2
  pos. correlated 1
  neg. correlated 1
List of 2 genes significantly correlated to 'PATHOLOGY.N.STAGE' by Spearman correlation test

Table S9.  Get Full Table List of 2 genes significantly correlated to 'PATHOLOGY.N.STAGE' by Spearman correlation test

SpearmanCorr corrP Q
POLR2J3__1 -0.2478 7.964e-07 0.0159
VAMP1 0.2385 2.09e-06 0.0418

Figure S4.  Get High-res Image As an example, this figure shows the association of POLR2J3__1 to 'PATHOLOGY.N.STAGE'. P value = 7.96e-07 with Spearman correlation analysis.

Clinical variable #6: 'PATHOLOGY.M.STAGE'

192 genes related to 'PATHOLOGY.M.STAGE'.

Table S10.  Basic characteristics of clinical feature: 'PATHOLOGY.M.STAGE'

PATHOLOGY.M.STAGE Labels N
  M0 259
  M1 12
  M1A 1
  M1B 3
  MX 117
     
  Significant markers N = 192
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'

ANOVA_P Q
PPP2R5B 7.676e-84 1.53e-79
C8ORF55 2.474e-61 4.95e-57
HOMER3 2.755e-38 5.51e-34
KILLIN 5.324e-30 1.06e-25
PTEN 5.324e-30 1.06e-25
POLR2J2 1.126e-28 2.25e-24
FBXL19 2.544e-28 5.09e-24
NCRNA00095 2.544e-28 5.09e-24
C14ORF19 6.169e-28 1.23e-23
ABHD15__1 9.197e-26 1.84e-21

Figure S5.  Get High-res Image As an example, this figure shows the association of PPP2R5B to 'PATHOLOGY.M.STAGE'. P value = 7.68e-84 with ANOVA analysis.

Clinical variable #7: 'GENDER'

98 genes related to 'GENDER'.

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

GENDER Labels N
  FEMALE 212
  MALE 184
     
  Significant markers N = 98
  Higher in MALE 10
  Higher in FEMALE 88
List of top 10 genes differentially expressed by 'GENDER'

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

T(pos if higher in 'MALE') ttestP Q AUC
KIF4B -13.97 5.664e-36 1.13e-31 0.8443
EIF4A1 -10.44 1.778e-22 3.55e-18 0.7895
SNORA48 -10.44 1.778e-22 3.55e-18 0.7895
RNASEH2C 8.42 7.343e-16 1.47e-11 0.7135
COX7C -8 1.833e-14 3.66e-10 0.729
FRG1B -7.79 6.207e-14 1.24e-09 0.7144
CCDC121__1 -7.64 1.84e-13 3.68e-09 0.7027
GPN1__1 -7.64 1.84e-13 3.68e-09 0.7027
TBCA -7.43 7.343e-13 1.47e-08 0.717
ATP5J 7.5 1.435e-12 2.87e-08 0.7345

Figure S6.  Get High-res Image As an example, this figure shows the association of KIF4B to 'GENDER'. P value = 5.66e-36 with T-test analysis.

Clinical variable #8: 'KARNOFSKY.PERFORMANCE.SCORE'

No gene related to 'KARNOFSKY.PERFORMANCE.SCORE'.

Table S14.  Basic characteristics of clinical feature: 'KARNOFSKY.PERFORMANCE.SCORE'

KARNOFSKY.PERFORMANCE.SCORE Mean (SD) 84.23 (22)
  Significant markers N = 0
Clinical variable #9: 'HISTOLOGICAL.TYPE'

102 genes related to 'HISTOLOGICAL.TYPE'.

Table S15.  Basic characteristics of clinical feature: 'HISTOLOGICAL.TYPE'

HISTOLOGICAL.TYPE Labels N
  LUNG ACINAR ADENOCARCINOMA 13
  LUNG ADENOCARCINOMA MIXED SUBTYPE 77
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) 251
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS 4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS 17
  LUNG CLEAR CELL ADENOCARCINOMA 1
  LUNG MICROPAPILLARY ADENOCARCINOMA 2
  LUNG MUCINOUS ADENOCARCINOMA 2
  LUNG PAPILLARY ADENOCARCINOMA 17
  LUNG SIGNET RING ADENOCARCINOMA 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA 4
  MUCINOUS (COLLOID) CARCINOMA 7
     
  Significant markers N = 102
List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'

Table S16.  Get Full Table List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'

ANOVA_P Q
DNAJC25-GNG10__1 3.026e-39 6.05e-35
GNG10 3.026e-39 6.05e-35
METTL2A 4.832e-39 9.66e-35
RAD9A 9.762e-39 1.95e-34
PDCD11 1.875e-29 3.75e-25
USMG5 1.875e-29 3.75e-25
MURC 2.906e-28 5.81e-24
MED17 1.606e-27 3.21e-23
CCDC126 3.359e-22 6.71e-18
KRT39 2.39e-19 4.78e-15

Figure S7.  Get High-res Image As an example, this figure shows the association of DNAJC25-GNG10__1 to 'HISTOLOGICAL.TYPE'. P value = 3.03e-39 with ANOVA analysis.

Clinical variable #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

64 genes related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

Table S17.  Basic characteristics of clinical feature: 'RADIATIONS.RADIATION.REGIMENINDICATION'

RADIATIONS.RADIATION.REGIMENINDICATION Labels N
  NO 18
  YES 378
     
  Significant markers N = 64
  Higher in YES 47
  Higher in NO 17
List of top 10 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

Table S18.  Get Full Table List of top 10 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

T(pos if higher in 'YES') ttestP Q AUC
NT5E 7.61 3.366e-13 6.73e-09 0.5797
KIAA1529 7.63 2.638e-12 5.27e-08 0.6458
GRIK4 7.19 6.805e-12 1.36e-07 0.668
ZNF642 6.98 1.384e-11 2.77e-07 0.6892
GALNT14 6.52 2.147e-10 4.29e-06 0.6039
HIST1H4J 6.52 3.071e-10 6.14e-06 0.6426
PRELP -6.43 5.487e-10 1.1e-05 0.6005
LMX1B 6.71 6.823e-10 1.36e-05 0.7136
H2AFJ 6.29 9.885e-10 1.98e-05 0.5647
EPHA3 6.49 1.267e-09 2.53e-05 0.679

Figure S8.  Get High-res Image As an example, this figure shows the association of NT5E to 'RADIATIONS.RADIATION.REGIMENINDICATION'. P value = 3.37e-13 with T-test analysis.

Clinical variable #11: 'NUMBERPACKYEARSSMOKED'

2 genes related to 'NUMBERPACKYEARSSMOKED'.

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

NUMBERPACKYEARSSMOKED Mean (SD) 41.21 (27)
  Significant markers N = 2
  pos. correlated 0
  neg. correlated 2
List of 2 genes significantly correlated to 'NUMBERPACKYEARSSMOKED' by Spearman correlation test

Table S20.  Get Full Table List of 2 genes significantly correlated to 'NUMBERPACKYEARSSMOKED' by Spearman correlation test

SpearmanCorr corrP Q
FAM128A__1 -0.3135 1.222e-07 0.00244
LOC150776__1 -0.3135 1.222e-07 0.00244

Figure S9.  Get High-res Image As an example, this figure shows the association of FAM128A__1 to 'NUMBERPACKYEARSSMOKED'. P value = 1.22e-07 with Spearman correlation analysis. The straight line presents the best linear regression.

Clinical variable #12: 'YEAROFTOBACCOSMOKINGONSET'

No gene related to 'YEAROFTOBACCOSMOKINGONSET'.

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

YEAROFTOBACCOSMOKINGONSET Mean (SD) 1965.27 (12)
  Significant markers N = 0
Clinical variable #13: 'COMPLETENESS.OF.RESECTION'

122 genes related to 'COMPLETENESS.OF.RESECTION'.

Table S22.  Basic characteristics of clinical feature: 'COMPLETENESS.OF.RESECTION'

COMPLETENESS.OF.RESECTION Labels N
  R0 261
  R1 8
  R2 1
  RX 15
     
  Significant markers N = 122
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'

ANOVA_P Q
DDX52 8.901e-185 1.78e-180
CCDC53 4.219e-141 8.43e-137
ANKIB1 1.015e-86 2.03e-82
KRIT1 1.015e-86 2.03e-82
SLC6A16 6.399e-57 1.28e-52
CWC22 2.147e-54 4.29e-50
ZBTB1 9.262e-54 1.85e-49
ZBTB25 9.262e-54 1.85e-49
HARBI1 1.882e-44 3.76e-40
KIAA0652__1 1.882e-44 3.76e-40

Figure S10.  Get High-res Image As an example, this figure shows the association of DDX52 to 'COMPLETENESS.OF.RESECTION'. P value = 8.9e-185 with ANOVA analysis.

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 = 396

  • Number of genes = 19992

  • Number of clinical features = 13

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

ANOVA analysis

For multi-class clinical features (ordinal or nominal), one-way analysis of variance (Howell 2002) was applied to compare the log2-expression levels between different clinical classes using 'anova' function in R

Student's t-test analysis

For two-class clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the log2-expression levels between the two clinical classes using 't.test' function in R

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] Howell, D, Statistical Methods for Psychology. (5th ed.), Duxbury Press:324-5 (2002)
[4] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[5] 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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