Stomach Adenocarcinoma: Correlation between mRNAseq expression and clinical features
(primary solid tumor cohort)
Maintained by Juok Cho (Broad Institute)
Overview
Introduction

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

Summary

Testing the association between 19433 genes and 10 clinical features across 43 samples, statistically thresholded by Q value < 0.05, 6 clinical features related to at least one genes.

  • 11 genes correlated to 'GENDER'.

    • XIST|7503_CALCULATED ,  USP9Y|8287_CALCULATED ,  TSIX|9383_CALCULATED ,  ZFY|7544_CALCULATED ,  PRKY|5616_CALCULATED ,  ...

  • 117 genes correlated to 'HISTOLOGICAL.TYPE'.

    • SEL1L|6400_CALCULATED ,  BIRC5|332_CALCULATED ,  EPR1|8475_CALCULATED ,  YAP1|10413_CALCULATED ,  BTBD6|90135_CALCULATED ,  ...

  • 2 genes correlated to 'PATHOLOGY.N'.

    • NKX2-2|4821_CALCULATED ,  PEX5L|51555_CALCULATED

  • 1 gene correlated to 'PATHOLOGICSPREAD(M)'.

    • DBR1|51163_CALCULATED

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

    • ZNF673|55634_CALCULATED ,  C5ORF25|375484_CALCULATED

  • 1 gene correlated to 'NUMBER.OF.LYMPH.NODES'.

    • GPATCH2|55105_CALCULATED

  • No genes correlated to 'Time to Death', 'AGE', 'PATHOLOGY.T', and 'TUMOR.STAGE'.

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=0        
GENDER t test N=11 male N=9 female N=2
HISTOLOGICAL TYPE ANOVA test N=117        
PATHOLOGY T Spearman correlation test   N=0        
PATHOLOGY N Spearman correlation test N=2 higher pN N=1 lower pN N=1
PATHOLOGICSPREAD(M) ANOVA test N=1        
TUMOR STAGE Spearman correlation test   N=0        
COMPLETENESS OF RESECTION ANOVA test N=2        
NUMBER OF LYMPH NODES Spearman correlation test N=1 higher number.of.lymph.nodes N=0 lower number.of.lymph.nodes N=1
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) 1-54 (median=14)
  censored N = 13
  death N = 5
     
  Significant markers N = 0
Clinical variable #2: 'AGE'

No gene related to 'AGE'.

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

AGE Mean (SD) 70.37 (10)
  Significant markers N = 0
Clinical variable #3: 'GENDER'

11 genes related to 'GENDER'.

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

GENDER Labels N
  FEMALE 20
  MALE 23
     
  Significant markers N = 11
  Higher in MALE 9
  Higher in FEMALE 2
List of top 10 genes differentially expressed by 'GENDER'

Table S4.  Get Full Table List of top 10 genes differentially expressed by 'GENDER'

T(pos if higher in 'MALE') ttestP Q AUC
XIST|7503_CALCULATED -19.68 5.119e-22 9.94e-18 1
USP9Y|8287_CALCULATED 28.46 3.31e-21 6.43e-17 1
TSIX|9383_CALCULATED -18.32 5.512e-21 1.07e-16 1
ZFY|7544_CALCULATED 22.33 4.944e-20 9.6e-16 1
PRKY|5616_CALCULATED 17.07 3.058e-17 5.94e-13 1
RPS4Y1|6192_CALCULATED 19.5 1.478e-15 2.87e-11 1
TMSB4Y|9087_CALCULATED 17.9 3.703e-15 7.19e-11 1
EIF1AY|9086_CALCULATED 20.73 1.294e-14 2.51e-10 1
KDM5D|8284_CALCULATED 23.59 1.51e-12 2.93e-08 1
UTY|7404_CALCULATED 19.54 1.591e-12 3.09e-08 1

Figure S1.  Get High-res Image As an example, this figure shows the association of XIST|7503_CALCULATED to 'GENDER'. P value = 5.12e-22 with T-test analysis.

Clinical variable #4: 'HISTOLOGICAL.TYPE'

117 genes related to 'HISTOLOGICAL.TYPE'.

Table S5.  Basic characteristics of clinical feature: 'HISTOLOGICAL.TYPE'

HISTOLOGICAL.TYPE Labels N
  STOMACH ADENOCARCINOMA - DIFFUSE TYPE 2
  STOMACH ADENOCARCINOMA - NOT OTHERWISE SPECIFIED (NOS) 25
  STOMACH INTESTINAL ADENOCARCINOMA - MUCINOUS TYPE 1
  STOMACH INTESTINAL ADENOCARCINOMA - TUBULAR TYPE 1
  STOMACH INTESTINAL ADENOCARCINOMA - TYPE NOT OTHERWISE SPECIFIED (NOS) 9
     
  Significant markers N = 117
List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'

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

ANOVA_P Q
SEL1L|6400_CALCULATED 7.396e-13 1.44e-08
BIRC5|332_CALCULATED 1.14e-11 2.22e-07
EPR1|8475_CALCULATED 3.636e-11 7.07e-07
YAP1|10413_CALCULATED 4.648e-11 9.03e-07
BTBD6|90135_CALCULATED 1.764e-10 3.43e-06
DLGAP5|9787_CALCULATED 4.193e-10 8.15e-06
TK1|7083_CALCULATED 6.594e-10 1.28e-05
REST|5978_CALCULATED 8.98e-10 1.74e-05
GRIK1|2897_CALCULATED 1.099e-09 2.13e-05
SPC25|57405_CALCULATED 1.494e-09 2.9e-05

Figure S2.  Get High-res Image As an example, this figure shows the association of SEL1L|6400_CALCULATED to 'HISTOLOGICAL.TYPE'. P value = 7.4e-13 with ANOVA analysis.

Clinical variable #5: 'PATHOLOGY.T'

No gene related to 'PATHOLOGY.T'.

Table S7.  Basic characteristics of clinical feature: 'PATHOLOGY.T'

PATHOLOGY.T Mean (SD) 2.74 (0.93)
  N
  T1 2
  T2 14
  T3 9
  T4 9
     
  Significant markers N = 0
Clinical variable #6: 'PATHOLOGY.N'

2 genes related to 'PATHOLOGY.N'.

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

PATHOLOGY.N Mean (SD) 1.22 (1)
  N
  N0 8
  N1 14
  N2 5
  N3 5
     
  Significant markers N = 2
  pos. correlated 1
  neg. correlated 1
List of 2 genes significantly correlated to 'PATHOLOGY.N' by Spearman correlation test

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

SpearmanCorr corrP Q
NKX2-2|4821_CALCULATED 0.8641 2.19e-07 0.00426
PEX5L|51555_CALCULATED -0.7489 1.933e-06 0.0376

Figure S3.  Get High-res Image As an example, this figure shows the association of NKX2-2|4821_CALCULATED to 'PATHOLOGY.N'. P value = 2.19e-07 with Spearman correlation analysis.

Clinical variable #7: 'PATHOLOGICSPREAD(M)'

One gene related to 'PATHOLOGICSPREAD(M)'.

Table S10.  Basic characteristics of clinical feature: 'PATHOLOGICSPREAD(M)'

PATHOLOGICSPREAD(M) Labels N
  M0 34
  M1 7
  MX 2
     
  Significant markers N = 1
List of one gene differentially expressed by 'PATHOLOGICSPREAD(M)'

Table S11.  Get Full Table List of one gene differentially expressed by 'PATHOLOGICSPREAD(M)'

ANOVA_P Q
DBR1|51163_CALCULATED 4.046e-07 0.00786

Figure S4.  Get High-res Image As an example, this figure shows the association of DBR1|51163_CALCULATED to 'PATHOLOGICSPREAD(M)'. P value = 4.05e-07 with ANOVA analysis.

Clinical variable #8: 'TUMOR.STAGE'

No gene related to 'TUMOR.STAGE'.

Table S12.  Basic characteristics of clinical feature: 'TUMOR.STAGE'

TUMOR.STAGE Mean (SD) 2.75 (1.2)
  N
  Stage 1 7
  Stage 2 4
  Stage 3 6
  Stage 4 11
     
  Significant markers N = 0
Clinical variable #9: 'COMPLETENESS.OF.RESECTION'

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

Table S13.  Basic characteristics of clinical feature: 'COMPLETENESS.OF.RESECTION'

COMPLETENESS.OF.RESECTION Labels N
  R0 13
  R1 1
  R2 7
  RX 22
     
  Significant markers N = 2
List of 2 genes differentially expressed by 'COMPLETENESS.OF.RESECTION'

Table S14.  Get Full Table List of 2 genes differentially expressed by 'COMPLETENESS.OF.RESECTION'

ANOVA_P Q
ZNF673|55634_CALCULATED 1.084e-11 2.11e-07
C5ORF25|375484_CALCULATED 2.035e-06 0.0395

Figure S5.  Get High-res Image As an example, this figure shows the association of ZNF673|55634_CALCULATED to 'COMPLETENESS.OF.RESECTION'. P value = 1.08e-11 with ANOVA analysis.

Clinical variable #10: 'NUMBER.OF.LYMPH.NODES'

One gene related to 'NUMBER.OF.LYMPH.NODES'.

Table S15.  Basic characteristics of clinical feature: 'NUMBER.OF.LYMPH.NODES'

NUMBER.OF.LYMPH.NODES Mean (SD) 2.82 (2.2)
  Significant markers N = 1
  pos. correlated 0
  neg. correlated 1
List of one gene significantly correlated to 'NUMBER.OF.LYMPH.NODES' by Spearman correlation test

Table S16.  Get Full Table List of one gene significantly correlated to 'NUMBER.OF.LYMPH.NODES' by Spearman correlation test

SpearmanCorr corrP Q
GPATCH2|55105_CALCULATED -0.963 2.002e-06 0.0387

Figure S6.  Get High-res Image As an example, this figure shows the association of GPATCH2|55105_CALCULATED to 'NUMBER.OF.LYMPH.NODES'. P value = 2e-06 with Spearman correlation analysis. The straight line presents the best linear regression.

Methods & Data
Input

  • Expresson data file = STAD-TP.mRNAseq_RPKM_log2.txt

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

  • Number of patients = 43

  • Number of genes = 19433

  • Number of clinical features = 10

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.

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] 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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