Glioblastoma Multiforme: Correlation between mRNA expression and clinical features
Maintained by TCGA GDAC Team (Broad Institute/Dana-Farber Cancer Institute/Harvard Medical School)
Overview
Introduction

This pipeline uses various statistical tests to identify mRNAs whose expression levels correlated to selected clinical features.

Summary

Testing the association between 12042 genes and 6 clinical features across 519 samples, statistically thresholded by Q value < 0.05, 5 clinical features related to at least one genes.

  • 21 genes correlated to 'Time to Death'.

    • CLEC5A ,  EFEMP2 ,  NCOA4 ,  ATP5C1 ,  DIRAS3 ,  ...

  • 76 genes correlated to 'AGE'.

    • RANBP17 ,  FBXO17 ,  TUSC3 ,  KIAA0495 ,  NOL3 ,  ...

  • 23 genes correlated to 'GENDER'.

    • DDX3Y ,  RPS4Y1 ,  JARID1D ,  EIF1AY ,  NLGN4Y ,  ...

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

    • NPAT ,  HOXD10

  • 14 genes correlated to 'NEOADJUVANT.THERAPY'.

    • WDR57 ,  SMU1 ,  SSNA1 ,  DNAJA2 ,  IDH3A ,  ...

  • No genes correlated to 'KARNOFSKY.PERFORMANCE.SCORE'

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=21 shorter survival N=11 longer survival N=10
AGE Spearman correlation test N=76 older N=42 younger N=34
GENDER t test N=23 male N=11 female N=12
KARNOFSKY PERFORMANCE SCORE Spearman correlation test   N=0        
RADIATIONS RADIATION REGIMENINDICATION t test N=2 yes N=1 no N=1
NEOADJUVANT THERAPY t test N=14 yes N=1 no N=13
Clinical variable #1: 'Time to Death'

21 genes related to 'Time to Death'.

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

Time to Death Duration (Months) 0.1-127.6 (median=9.9)
  censored N = 116
  death N = 403
     
  Significant markers N = 21
  associated with shorter survival 11
  associated with longer survival 10
List of top 10 genes significantly associated with 'Time to Death' by Cox regression test

Table S2.  Get Full Table List of top 10 genes significantly associated with 'Time to Death' by Cox regression test

HazardRatio Wald_P Q C_index
CLEC5A 1.23 7.107e-08 0.00086 0.584
EFEMP2 1.3 7.708e-08 0.00093 0.542
NCOA4 0.56 8.196e-08 0.00099 0.442
ATP5C1 0.59 8.228e-08 0.00099 0.451
DIRAS3 1.22 1.111e-07 0.0013 0.558
RANBP17 0.46 1.833e-07 0.0022 0.427
ANKRD26 0.39 2.458e-07 0.003 0.446
HIST3H2A 0.82 3.552e-07 0.0043 0.427
ZIC3 0.48 6.625e-07 0.008 0.444
FZD7 1.23 1.054e-06 0.013 0.556

Figure S1.  Get High-res Image As an example, this figure shows the association of CLEC5A to 'Time to Death'. four curves present the cumulative survival rates of 4 quartile subsets of patients. P value = 7.11e-08 with univariate Cox regression analysis using continuous log-2 expression values.

Clinical variable #2: 'AGE'

76 genes related to 'AGE'.

Table S3.  Basic characteristics of clinical feature: 'AGE'

AGE Mean (SD) 57.68 (14)
  Significant markers N = 76
  pos. correlated 42
  neg. correlated 34
List of top 10 genes significantly correlated to 'AGE' by Spearman correlation test

Table S4.  Get Full Table List of top 10 genes significantly correlated to 'AGE' by Spearman correlation test

SpearmanCorr corrP Q
RANBP17 -0.316 1.677e-13 2.02e-09
FBXO17 0.3024 1.966e-12 2.37e-08
TUSC3 -0.2972 4.787e-12 5.76e-08
KIAA0495 0.279 9.796e-11 1.18e-06
NOL3 0.2745 2.002e-10 2.41e-06
PPA1 -0.2725 2.734e-10 3.29e-06
H2AFY2 -0.2638 1.037e-09 1.25e-05
DRG2 0.2628 1.203e-09 1.45e-05
NCOA4 -0.2621 1.343e-09 1.62e-05
ENOSF1 -0.2585 2.273e-09 2.73e-05

Figure S2.  Get High-res Image As an example, this figure shows the association of RANBP17 to 'AGE'. P value = 1.68e-13 with Spearman correlation analysis. The straight line presents the best linear regression.

Clinical variable #3: 'GENDER'

23 genes related to 'GENDER'.

Table S5.  Basic characteristics of clinical feature: 'GENDER'

GENDER Labels N
  FEMALE 204
  MALE 315
     
  Significant markers N = 23
  Higher in MALE 11
  Higher in FEMALE 12
List of top 10 genes differentially expressed by 'GENDER'

Table S6.  Get Full Table List of top 10 genes differentially expressed by 'GENDER'

T(pos if higher in 'MALE') ttestP Q AUC
DDX3Y 37.55 8.529e-142 1.03e-137 0.96
RPS4Y1 40.23 7.983e-140 9.61e-136 0.9521
JARID1D 34.79 1.118e-136 1.35e-132 0.9603
EIF1AY 34.88 6.512e-134 7.84e-130 0.9536
NLGN4Y 30.85 4.165e-117 5.01e-113 0.9485
USP9Y 21.13 1.174e-71 1.41e-67 0.917
CYORF15B 19.36 3.851e-63 4.64e-59 0.9038
UTY 19.74 4.402e-60 5.3e-56 0.8998
ZFX -12.48 7.793e-30 9.38e-26 0.8205
HDHD1A -12.39 1.389e-29 1.67e-25 0.8043

Figure S3.  Get High-res Image As an example, this figure shows the association of DDX3Y to 'GENDER'. P value = 8.53e-142 with T-test analysis.

Clinical variable #4: 'KARNOFSKY.PERFORMANCE.SCORE'

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

Table S7.  Basic characteristics of clinical feature: 'KARNOFSKY.PERFORMANCE.SCORE'

KARNOFSKY.PERFORMANCE.SCORE Mean (SD) 77.12 (14)
  Significant markers N = 0
Clinical variable #5: 'RADIATIONS.RADIATION.REGIMENINDICATION'

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

Table S8.  Basic characteristics of clinical feature: 'RADIATIONS.RADIATION.REGIMENINDICATION'

RADIATIONS.RADIATION.REGIMENINDICATION Labels N
  NO 348
  YES 171
     
  Significant markers N = 2
  Higher in YES 1
  Higher in NO 1
List of 2 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

Table S9.  Get Full Table List of 2 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

T(pos if higher in 'YES') ttestP Q AUC
NPAT -5.56 5.006e-08 0.000603 0.6305
HOXD10 4.82 2.303e-06 0.0277 0.6291

Figure S4.  Get High-res Image As an example, this figure shows the association of NPAT to 'RADIATIONS.RADIATION.REGIMENINDICATION'. P value = 5.01e-08 with T-test analysis.

Clinical variable #6: 'NEOADJUVANT.THERAPY'

14 genes related to 'NEOADJUVANT.THERAPY'.

Table S10.  Basic characteristics of clinical feature: 'NEOADJUVANT.THERAPY'

NEOADJUVANT.THERAPY Labels N
  NO 270
  YES 249
     
  Significant markers N = 14
  Higher in YES 1
  Higher in NO 13
List of top 10 genes differentially expressed by 'NEOADJUVANT.THERAPY'

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

T(pos if higher in 'YES') ttestP Q AUC
WDR57 -6.05 2.736e-09 3.29e-05 0.6489
SMU1 -5.77 1.398e-08 0.000168 0.6361
SSNA1 -5.53 4.976e-08 0.000599 0.644
DNAJA2 -5.35 1.352e-07 0.00163 0.6379
IDH3A -5.3 1.714e-07 0.00206 0.6326
PDCL -5.17 3.275e-07 0.00394 0.6353
RPN1 -5.16 3.483e-07 0.00419 0.63
NUTF2 -4.96 9.692e-07 0.0117 0.6156
DNAJC17 -4.8 2.04e-06 0.0246 0.6223
CDK9 -4.78 2.305e-06 0.0277 0.6265

Figure S5.  Get High-res Image As an example, this figure shows the association of WDR57 to 'NEOADJUVANT.THERAPY'. P value = 2.74e-09 with T-test analysis.

Methods & Data
Input

  • Expresson data file = GBM.medianexp.txt

  • Clinical data file = GBM.clin.merged.picked.txt

  • Number of patients = 519

  • Number of genes = 12042

  • Number of clinical features = 6

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

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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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] 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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