Correlation between gene methylation status and clinical features
Stomach Adenocarcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C15T3HVF
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between gene methylation status and clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C15T3HVF
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 19809 genes and 11 clinical features across 260 samples, statistically thresholded by Q value < 0.05, 8 clinical features related to at least one genes.

  • 52 genes correlated to 'AGE'.

    • CGB1 ,  SNAR-G1 ,  CDCA5__1 ,  ZFPL1 ,  TOP1MT ,  ...

  • 606 genes correlated to 'NEOPLASM.DISEASESTAGE'.

    • DSTYK ,  CNN2 ,  EIF4G3 ,  ALDH6A1 ,  LIN52 ,  ...

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

    • EVPLL ,  RAB26 ,  PPAP2C ,  LNX1 ,  S100A2 ,  ...

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

    • RAB8A ,  MTIF2 ,  ATF2 ,  MIR933 ,  CYP4V2 ,  ...

  • 6 genes correlated to 'GENDER'.

    • KIF4B ,  ALG11__1 ,  UTP14C ,  GPX1 ,  CHTF8 ,  ...

  • 128 genes correlated to 'HISTOLOGICAL.TYPE'.

    • MIR568 ,  CREB1 ,  DTX4 ,  SLC23A1 ,  GPR39 ,  ...

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

    • FSCN1 ,  ARHGAP18 ,  CBWD1 ,  HAR1A ,  HAR1B ,  ...

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

    • RAB8A ,  CEBPD ,  BCAS3 ,  FDX1 ,  AHI1 ,  ...

  • No genes correlated to 'Time to Death', 'PATHOLOGY.N.STAGE', and 'NUMBER.OF.LYMPH.NODES'.

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=52 older N=1 younger N=51
NEOPLASM DISEASESTAGE ANOVA test N=606        
PATHOLOGY T STAGE Spearman correlation test N=513 higher stage N=311 lower stage N=202
PATHOLOGY N STAGE Spearman correlation test   N=0        
PATHOLOGY M STAGE ANOVA test N=34        
GENDER t test N=6 male N=4 female N=2
HISTOLOGICAL TYPE ANOVA test N=128        
RADIATIONS RADIATION REGIMENINDICATION t test N=693 yes N=657 no N=36
COMPLETENESS OF RESECTION ANOVA test N=554        
NUMBER OF LYMPH NODES Spearman correlation test   N=0        
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) 0.1-72.2 (median=1.3)
  censored N = 225
  death N = 20
     
  Significant markers N = 0
Clinical variable #2: 'AGE'

52 genes related to 'AGE'.

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

AGE Mean (SD) 65.33 (11)
  Significant markers N = 52
  pos. correlated 1
  neg. correlated 51
List of top 10 genes significantly correlated to 'AGE' by Spearman correlation test

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

SpearmanCorr corrP Q
CGB1 -0.3376 4.168e-08 0.000826
SNAR-G1 -0.3376 4.168e-08 0.000826
CDCA5__1 -0.3348 5.462e-08 0.00108
ZFPL1 -0.3348 5.462e-08 0.00108
TOP1MT -0.3344 5.703e-08 0.00113
SPRR1A -0.328 1.045e-07 0.00207
SLC26A3 -0.3265 1.21e-07 0.0024
PRTN3 -0.3234 1.617e-07 0.0032
SHMT1 -0.3191 2.386e-07 0.00472
CENPP__2 -0.319 2.415e-07 0.00478

Figure S1.  Get High-res Image As an example, this figure shows the association of CGB1 to 'AGE'. P value = 4.17e-08 with Spearman correlation analysis. The straight line presents the best linear regression.

Clinical variable #3: 'NEOPLASM.DISEASESTAGE'

606 genes related to 'NEOPLASM.DISEASESTAGE'.

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

NEOPLASM.DISEASESTAGE Labels N
  STAGE I 2
  STAGE IA 10
  STAGE IB 21
  STAGE II 25
  STAGE IIA 32
  STAGE IIB 42
  STAGE III 2
  STAGE IIIA 41
  STAGE IIIB 37
  STAGE IIIC 28
  STAGE IV 18
     
  Significant markers N = 606
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
DSTYK 1.252e-29 2.48e-25
CNN2 6.206e-26 1.23e-21
EIF4G3 3.242e-25 6.42e-21
ALDH6A1 9.843e-18 1.95e-13
LIN52 9.843e-18 1.95e-13
SMEK1 3.684e-14 7.3e-10
KDM3A 2.957e-13 5.86e-09
ABCC4 1.07e-12 2.12e-08
RILPL2 5.558e-12 1.1e-07
ASH2L 1.555e-11 3.08e-07

Figure S2.  Get High-res Image As an example, this figure shows the association of DSTYK to 'NEOPLASM.DISEASESTAGE'. P value = 1.25e-29 with ANOVA analysis.

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

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

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

PATHOLOGY.T.STAGE Mean (SD) 2.97 (0.83)
  N
  1 11
  2 59
  3 114
  4 74
     
  Significant markers N = 513
  pos. correlated 311
  neg. correlated 202
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
EVPLL 0.4179 2.515e-12 4.98e-08
RAB26 0.4067 1.075e-11 2.13e-07
PPAP2C 0.3828 1.969e-10 3.9e-06
LNX1 0.3816 2.282e-10 4.52e-06
S100A2 0.374 5.449e-10 1.08e-05
FAM3C -0.3692 9.43e-10 1.87e-05
UBL5 -0.3674 1.149e-09 2.27e-05
FFAR2 0.3671 1.186e-09 2.35e-05
PVRL4 0.3641 1.652e-09 3.27e-05
CGB8 0.3653 1.943e-09 3.85e-05

Figure S3.  Get High-res Image As an example, this figure shows the association of EVPLL to 'PATHOLOGY.T.STAGE'. P value = 2.52e-12 with Spearman correlation analysis.

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

No gene related to 'PATHOLOGY.N.STAGE'.

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

PATHOLOGY.N.STAGE Mean (SD) 1.22 (1.1)
  N
  0 90
  1 69
  2 49
  3 49
     
  Significant markers N = 0
Clinical variable #6: 'PATHOLOGY.M.STAGE'

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

Table S9.  Basic characteristics of clinical feature: 'PATHOLOGY.M.STAGE'

PATHOLOGY.M.STAGE Labels N
  M0 233
  M1 13
  MX 12
     
  Significant markers N = 34
List of top 10 genes differentially expressed by 'PATHOLOGY.M.STAGE'

Table S10.  Get Full Table List of top 10 genes differentially expressed by 'PATHOLOGY.M.STAGE'

ANOVA_P Q
RAB8A 8.378e-10 1.66e-05
MTIF2 2.067e-08 0.000409
ATF2 3.196e-08 0.000633
MIR933 3.196e-08 0.000633
CYP4V2 4.83e-08 0.000957
FDX1 4.916e-08 0.000974
RPS21 1.552e-07 0.00307
CCDC76__1 1.569e-07 0.00311
SASS6 1.569e-07 0.00311
SLC25A2 1.585e-07 0.00314

Figure S4.  Get High-res Image As an example, this figure shows the association of RAB8A to 'PATHOLOGY.M.STAGE'. P value = 8.38e-10 with ANOVA analysis.

Clinical variable #7: 'GENDER'

6 genes related to 'GENDER'.

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

GENDER Labels N
  FEMALE 97
  MALE 161
     
  Significant markers N = 6
  Higher in MALE 4
  Higher in FEMALE 2
List of 6 genes differentially expressed by 'GENDER'

Table S12.  Get Full Table List of 6 genes differentially expressed by 'GENDER'

T(pos if higher in 'MALE') ttestP Q AUC
KIF4B -12.48 5.094e-28 1.01e-23 0.8608
ALG11__1 13.58 1.974e-25 3.91e-21 0.9425
UTP14C 13.58 1.974e-25 3.91e-21 0.9425
GPX1 -7.87 1.755e-13 3.48e-09 0.7882
CHTF8 6.03 1.082e-08 0.000214 0.7732
HAS3 6.03 1.082e-08 0.000214 0.7732

Figure S5.  Get High-res Image As an example, this figure shows the association of KIF4B to 'GENDER'. P value = 5.09e-28 with T-test analysis.

Clinical variable #8: 'HISTOLOGICAL.TYPE'

128 genes related to 'HISTOLOGICAL.TYPE'.

Table S13.  Basic characteristics of clinical feature: 'HISTOLOGICAL.TYPE'

HISTOLOGICAL.TYPE Labels N
  STOMACH ADENOCARCINOMA DIFFUSE TYPE 44
  STOMACH ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) 116
  STOMACH INTESTINAL ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) 36
  STOMACH INTESTINAL ADENOCARCINOMA TUBULAR TYPE 39
  STOMACH INTESTINAL ADENOCARCINOMA  MUCINOUS TYPE 14
  STOMACH INTESTINAL ADENOCARCINOMA  PAPILLARY TYPE 6
  STOMACH ADENOCARCINOMA SIGNET RING TYPE 3
     
  Significant markers N = 128
List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'

Table S14.  Get Full Table List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'

ANOVA_P Q
MIR568 2.713e-13 5.37e-09
CREB1 5.478e-11 1.08e-06
DTX4 1.823e-09 3.61e-05
SLC23A1 2.026e-09 4.01e-05
GPR39 1.175e-08 0.000233
BRDT 1.42e-08 0.000281
ASB14 1.432e-08 0.000284
C20ORF151 1.617e-08 0.00032
BCL2L12__1 2.112e-08 0.000418
IRF3 2.112e-08 0.000418

Figure S6.  Get High-res Image As an example, this figure shows the association of MIR568 to 'HISTOLOGICAL.TYPE'. P value = 2.71e-13 with ANOVA analysis.

Clinical variable #9: 'RADIATIONS.RADIATION.REGIMENINDICATION'

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

Table S15.  Basic characteristics of clinical feature: 'RADIATIONS.RADIATION.REGIMENINDICATION'

RADIATIONS.RADIATION.REGIMENINDICATION Labels N
  NO 7
  YES 253
     
  Significant markers N = 693
  Higher in YES 657
  Higher in NO 36
List of top 10 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

Table S16.  Get Full Table List of top 10 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

T(pos if higher in 'YES') ttestP Q AUC
FSCN1 14.67 1.393e-35 2.76e-31 0.8103
ARHGAP18 13.68 2.772e-32 5.49e-28 0.9283
CBWD1 15.15 7.01e-31 1.39e-26 0.9311
HAR1A 12.8 4.214e-25 8.35e-21 0.8182
HAR1B 12.8 4.214e-25 8.35e-21 0.8182
PTPN18 11.54 1.227e-24 2.43e-20 0.786
HAR1A__1 11.39 7.535e-24 1.49e-19 0.6488
HAR1B__1 11.39 7.535e-24 1.49e-19 0.6488
TSPAN5 11.05 1.7e-23 3.37e-19 0.7516
DMC1 10.84 1.018e-22 2.02e-18 0.7753

Figure S7.  Get High-res Image As an example, this figure shows the association of FSCN1 to 'RADIATIONS.RADIATION.REGIMENINDICATION'. P value = 1.39e-35 with T-test analysis.

Clinical variable #10: 'COMPLETENESS.OF.RESECTION'

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

Table S17.  Basic characteristics of clinical feature: 'COMPLETENESS.OF.RESECTION'

COMPLETENESS.OF.RESECTION Labels N
  R0 225
  R1 9
  R2 5
     
  Significant markers N = 554
List of top 10 genes differentially expressed by 'COMPLETENESS.OF.RESECTION'

Table S18.  Get Full Table List of top 10 genes differentially expressed by 'COMPLETENESS.OF.RESECTION'

ANOVA_P Q
RAB8A 2.947e-18 5.84e-14
CEBPD 2.564e-17 5.08e-13
BCAS3 8.839e-17 1.75e-12
FDX1 1.748e-16 3.46e-12
AHI1 2.442e-16 4.84e-12
C6ORF217 2.442e-16 4.84e-12
GSG2 3.715e-16 7.36e-12
ITGAE__1 3.715e-16 7.36e-12
FBXO24 8.873e-16 1.76e-11
LRCH4__1 8.873e-16 1.76e-11

Figure S8.  Get High-res Image As an example, this figure shows the association of RAB8A to 'COMPLETENESS.OF.RESECTION'. P value = 2.95e-18 with ANOVA analysis.

Clinical variable #11: 'NUMBER.OF.LYMPH.NODES'

No gene related to 'NUMBER.OF.LYMPH.NODES'.

Table S19.  Basic characteristics of clinical feature: 'NUMBER.OF.LYMPH.NODES'

NUMBER.OF.LYMPH.NODES Mean (SD) 4.85 (7.3)
  Significant markers N = 0
Methods & Data
Input

  • Expresson data file = STAD-TP.meth.by_min_expr_corr.data.txt

  • Clinical data file = STAD-TP.clin.merged.picked.txt

  • Number of patients = 260

  • Number of genes = 19809

  • Number of clinical features = 11

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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