Correlation between gene methylation status and clinical features
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 16900 genes and 4 clinical features across 56 samples, statistically thresholded by Q value < 0.05, 3 clinical features related to at least one genes.

  • 2 genes correlated to 'AGE'.

    • PPTC7 ,  ZNF311

  • 1 gene correlated to 'GENDER'.

    • UTP14C

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

    • SEPSECS ,  C5ORF42 ,  KDELC1 ,  GOLGA7 ,  IREB2 ,  ...

  • No genes correlated to 'Time to Death'

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=2 older N=0 younger N=2
GENDER t test N=1 male N=1 female N=0
COMPLETENESS OF RESECTION ANOVA test N=8        
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) 0.1-83.6 (median=13.8)
  censored N = 31
  death N = 20
     
  Significant markers N = 0
Clinical variable #2: 'AGE'

2 genes related to 'AGE'.

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

AGE Mean (SD) 58.56 (15)
  Significant markers N = 2
  pos. correlated 0
  neg. correlated 2
List of 2 genes significantly correlated to 'AGE' by Spearman correlation test

Table S3.  Get Full Table List of 2 genes significantly correlated to 'AGE' by Spearman correlation test

SpearmanCorr corrP Q
PPTC7 -0.5951 1.657e-06 0.028
ZNF311 -0.5901 2.121e-06 0.0358

Figure S1.  Get High-res Image As an example, this figure shows the association of PPTC7 to 'AGE'. P value = 1.66e-06 with Spearman correlation analysis. The straight line presents the best linear regression.

Clinical variable #3: 'GENDER'

One gene related to 'GENDER'.

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

GENDER Labels N
  FEMALE 21
  MALE 35
     
  Significant markers N = 1
  Higher in MALE 1
  Higher in FEMALE 0
List of one gene differentially expressed by 'GENDER'

Table S5.  Get Full Table List of one gene differentially expressed by 'GENDER'

T(pos if higher in 'MALE') ttestP Q AUC
UTP14C 8.17 2.139e-08 0.000361 0.9456

Figure S2.  Get High-res Image As an example, this figure shows the association of UTP14C to 'GENDER'. P value = 2.14e-08 with T-test analysis.

Clinical variable #4: 'COMPLETENESS.OF.RESECTION'

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

Table S6.  Basic characteristics of clinical feature: 'COMPLETENESS.OF.RESECTION'

COMPLETENESS.OF.RESECTION Labels N
  R0 42
  R1 4
  R2 1
  RX 6
     
  Significant markers N = 8
List of 8 genes differentially expressed by 'COMPLETENESS.OF.RESECTION'

Table S7.  Get Full Table List of 8 genes differentially expressed by 'COMPLETENESS.OF.RESECTION'

ANOVA_P Q
SEPSECS 3.171e-37 5.36e-33
C5ORF42 3.664e-13 6.19e-09
KDELC1 5.313e-10 8.98e-06
GOLGA7 2.808e-09 4.74e-05
IREB2 4.829e-08 0.000816
C4ORF12 1.411e-07 0.00238
MGMT 5.062e-07 0.00855
SEPT2 1.797e-06 0.0304

Figure S3.  Get High-res Image As an example, this figure shows the association of SEPSECS to 'COMPLETENESS.OF.RESECTION'. P value = 3.17e-37 with ANOVA analysis.

Methods & Data
Input

  • Expresson data file = LIHC-TP.meth.for_correlation.filtered_data.txt

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

  • Number of patients = 56

  • Number of genes = 16900

  • Number of clinical features = 4

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

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

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

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.

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