Correlation between mRNAseq expression and clinical features
Esophageal Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1NC60KN
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between mRNAseq expression and clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1NC60KN
Overview
Introduction

This pipeline uses various statistical tests to identify mRNAs whose log2 expression levels correlated to selected clinical features. The input file "ESCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt" is generated in the pipeline mRNAseq_Preprocess in the stddata run.

Summary

Testing the association between 18768 genes and 15 clinical features across 184 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 11 clinical features related to at least one genes.

  • 3 genes correlated to 'DAYS_TO_DEATH_OR_LAST_FUP'.

    • ENTPD4|9583 ,  CXCL10|3627 ,  C10ORF128|170371

  • 30 genes correlated to 'YEARS_TO_BIRTH'.

    • HAT1|8520 ,  CENPA|1058 ,  MCM2|4171 ,  POLQ|10721 ,  RIPK3|11035 ,  ...

  • 30 genes correlated to 'PATHOLOGIC_STAGE'.

    • RPLP0P2|113157 ,  CHN2|1124 ,  GPR160|26996 ,  SUSD1|64420 ,  FZD5|7855 ,  ...

  • 30 genes correlated to 'PATHOLOGY_T_STAGE'.

    • SI|6476 ,  CTHRC1|115908 ,  ARL4C|10123 ,  NAP1L1|4673 ,  LOC399959|399959 ,  ...

  • 30 genes correlated to 'PATHOLOGY_N_STAGE'.

    • ZDHHC23|254887 ,  CMTM8|152189 ,  GPR160|26996 ,  AQP11|282679 ,  NDE1|54820 ,  ...

  • 2 genes correlated to 'GENDER'.

    • CYORF15B|84663 ,  CA5BP|340591

  • 30 genes correlated to 'RADIATION_THERAPY'.

    • LOC151534|151534 ,  CDX1|1044 ,  INPP5J|27124 ,  KRT18|3875 ,  LGALS4|3960 ,  ...

  • 30 genes correlated to 'KARNOFSKY_PERFORMANCE_SCORE'.

    • EIF3F|8665 ,  EEF1A1P9|441032 ,  RPL10A|4736 ,  EEA1|8411 ,  MT1F|4494 ,  ...

  • 30 genes correlated to 'HISTOLOGICAL_TYPE'.

    • SEMA4G|57715 ,  C11ORF9|745 ,  TMC5|79838 ,  PLEKHA6|22874 ,  CDHR5|53841 ,  ...

  • 30 genes correlated to 'NUMBER_PACK_YEARS_SMOKED'.

    • SF3B14|51639 ,  ZMYND19|116225 ,  CCPG1|9236 ,  NIT2|56954 ,  LOC100125556|100125556 ,  ...

  • 30 genes correlated to 'RACE'.

    • TMTC3|160418 ,  BCL2L1|598 ,  LRP12|29967 ,  TP63|8626 ,  CHODL|140578 ,  ...

  • No genes correlated to 'PATHOLOGY_M_STAGE', 'RESIDUAL_TUMOR', 'NUMBER_OF_LYMPH_NODES', and 'ETHNICITY'.

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 P value < 0.05 and Q value < 0.3.

Clinical feature Statistical test Significant genes Associated with                 Associated with
DAYS_TO_DEATH_OR_LAST_FUP Cox regression test N=3   N=NA   N=NA
YEARS_TO_BIRTH Spearman correlation test N=30 older N=11 younger N=19
PATHOLOGIC_STAGE Kruskal-Wallis test N=30        
PATHOLOGY_T_STAGE Spearman correlation test N=30 higher stage N=23 lower stage N=7
PATHOLOGY_N_STAGE Spearman correlation test N=30 higher stage N=23 lower stage N=7
PATHOLOGY_M_STAGE Wilcoxon test   N=0        
GENDER Wilcoxon test N=2 male N=2 female N=0
RADIATION_THERAPY Wilcoxon test N=30 yes N=30 no N=0
KARNOFSKY_PERFORMANCE_SCORE Spearman correlation test N=30 higher score N=25 lower score N=5
HISTOLOGICAL_TYPE Wilcoxon test N=30 esophagus squamous cell carcinoma N=30 esophagus adenocarcinoma, nos N=0
NUMBER_PACK_YEARS_SMOKED Spearman correlation test N=30 higher number_pack_years_smoked N=10 lower number_pack_years_smoked N=20
RESIDUAL_TUMOR Kruskal-Wallis test   N=0        
NUMBER_OF_LYMPH_NODES Spearman correlation test   N=0        
RACE Kruskal-Wallis test N=30        
ETHNICITY Wilcoxon test   N=0        
Clinical variable #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

3 genes related to 'DAYS_TO_DEATH_OR_LAST_FUP'.

Table S1.  Basic characteristics of clinical feature: 'DAYS_TO_DEATH_OR_LAST_FUP'

DAYS_TO_DEATH_OR_LAST_FUP Duration (Months) 0.1-122.1 (median=12.9)
  censored N = 106
  death N = 77
     
  Significant markers N = 3
  associated with shorter survival NA
  associated with longer survival NA
List of 3 genes differentially expressed by 'DAYS_TO_DEATH_OR_LAST_FUP'

Table S2.  Get Full Table List of 3 genes significantly associated with 'Time to Death' by Cox regression test. For the survival curves, it compared quantile intervals at c(0, 0.25, 0.50, 0.75, 1) and did not try survival analysis if there is only one interval.

logrank_P Q C_index
ENTPD4|9583 5.84e-07 0.011 0.458
CXCL10|3627 1.44e-05 0.14 0.571
C10ORF128|170371 3.99e-05 0.25 0.519
Clinical variable #2: 'YEARS_TO_BIRTH'

30 genes related to 'YEARS_TO_BIRTH'.

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

YEARS_TO_BIRTH Mean (SD) 62.46 (12)
  Significant markers N = 30
  pos. correlated 11
  neg. correlated 19
List of top 10 genes differentially expressed by 'YEARS_TO_BIRTH'

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

SpearmanCorr corrP Q
HAT1|8520 -0.4768 7.778e-12 1.46e-07
CENPA|1058 -0.4465 2.108e-10 1.98e-06
MCM2|4171 -0.4414 3.564e-10 2.23e-06
POLQ|10721 -0.4375 5.275e-10 2.47e-06
RIPK3|11035 0.4323 8.936e-10 3.1e-06
RFC4|5984 -0.4298 1.134e-09 3.1e-06
TMC5|79838 0.4307 1.157e-09 3.1e-06
C3ORF37|56941 -0.4279 1.375e-09 3.23e-06
SPNS2|124976 0.423 2.208e-09 4.61e-06
ALDH3B1|221 0.421 2.669e-09 4.75e-06
Clinical variable #3: 'PATHOLOGIC_STAGE'

30 genes related to 'PATHOLOGIC_STAGE'.

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

PATHOLOGIC_STAGE Labels N
  STAGE I 8
  STAGE IA 5
  STAGE IB 6
  STAGE II 1
  STAGE IIA 46
  STAGE IIB 31
  STAGE III 26
  STAGE IIIA 14
  STAGE IIIB 9
  STAGE IIIC 7
  STAGE IV 5
  STAGE IVA 4
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'PATHOLOGIC_STAGE'

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

kruskal_wallis_P Q
RPLP0P2|113157 3.355e-06 0.014
CHN2|1124 3.668e-06 0.014
GPR160|26996 5.839e-06 0.014
SUSD1|64420 6.923e-06 0.014
FZD5|7855 8.106e-06 0.014
HTRA3|94031 8.505e-06 0.014
MMP15|4324 8.511e-06 0.014
PDX1|3651 8.902e-06 0.014
PRR15|222171 9.129e-06 0.014
GPNMB|10457 1.018e-05 0.014
Clinical variable #4: 'PATHOLOGY_T_STAGE'

30 genes related to 'PATHOLOGY_T_STAGE'.

Table S7.  Basic characteristics of clinical feature: 'PATHOLOGY_T_STAGE'

PATHOLOGY_T_STAGE Mean (SD) 2.39 (0.84)
  N
  T0 1
  T1 31
  T2 42
  T3 88
  T4 5
     
  Significant markers N = 30
  pos. correlated 23
  neg. correlated 7
List of top 10 genes differentially expressed by 'PATHOLOGY_T_STAGE'

Table S8.  Get Full Table List of top 10 genes significantly correlated to 'PATHOLOGY_T_STAGE' by Spearman correlation test

SpearmanCorr corrP Q
SI|6476 -0.4953 3.351e-07 0.00498
CTHRC1|115908 0.3708 8.081e-07 0.00498
ARL4C|10123 0.3684 9.632e-07 0.00498
NAP1L1|4673 0.3623 1.504e-06 0.00498
LOC399959|399959 0.3616 1.581e-06 0.00498
TMEM45B|120224 -0.3606 1.693e-06 0.00498
ACOT11|26027 -0.3591 1.878e-06 0.00498
NPTX1|4884 0.3604 2.291e-06 0.00498
FLJ16779|100192386 0.3659 2.838e-06 0.00498
CLCN3|1182 -0.3498 3.597e-06 0.00498
Clinical variable #5: 'PATHOLOGY_N_STAGE'

30 genes related to 'PATHOLOGY_N_STAGE'.

Table S9.  Basic characteristics of clinical feature: 'PATHOLOGY_N_STAGE'

PATHOLOGY_N_STAGE Mean (SD) 0.71 (0.8)
  N
  N0 76
  N1 69
  N2 12
  N3 8
     
  Significant markers N = 30
  pos. correlated 23
  neg. correlated 7
List of top 10 genes differentially expressed by 'PATHOLOGY_N_STAGE'

Table S10.  Get Full Table List of top 10 genes significantly correlated to 'PATHOLOGY_N_STAGE' by Spearman correlation test

SpearmanCorr corrP Q
ZDHHC23|254887 0.3583 2.305e-06 0.0298
CMTM8|152189 0.3536 3.179e-06 0.0298
GPR160|26996 0.3459 5.337e-06 0.0334
AQP11|282679 0.3398 8.013e-06 0.0376
NDE1|54820 -0.3354 1.064e-05 0.04
C6ORF136|221545 0.3195 2.877e-05 0.0628
TTC23|64927 -0.3188 2.994e-05 0.0628
CLDN3|1365 0.3163 3.501e-05 0.0628
PNMT|5409 0.3284 4.089e-05 0.0628
C20ORF118|140711 0.3133 4.187e-05 0.0628
Clinical variable #6: 'PATHOLOGY_M_STAGE'

No gene related to 'PATHOLOGY_M_STAGE'.

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

PATHOLOGY_M_STAGE Labels N
  class0 135
  class1 9
     
  Significant markers N = 0
Clinical variable #7: 'GENDER'

2 genes related to 'GENDER'.

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

GENDER Labels N
  FEMALE 26
  MALE 158
     
  Significant markers N = 2
  Higher in MALE 2
  Higher in FEMALE 0
List of 2 genes differentially expressed by 'GENDER'

Table S13.  Get Full Table List of 2 genes differentially expressed by 'GENDER'. 16 significant gene(s) located in sex chromosomes is(are) filtered out.

W(pos if higher in 'MALE') wilcoxontestP Q AUC
CYORF15B|84663 948 3.364e-05 0.0486 1
CA5BP|340591 1072 9.614e-05 0.129 0.739
Clinical variable #8: 'RADIATION_THERAPY'

30 genes related to 'RADIATION_THERAPY'.

Table S14.  Basic characteristics of clinical feature: 'RADIATION_THERAPY'

RADIATION_THERAPY Labels N
  NO 123
  YES 43
     
  Significant markers N = 30
  Higher in YES 30
  Higher in NO 0
List of top 10 genes differentially expressed by 'RADIATION_THERAPY'

Table S15.  Get Full Table List of top 10 genes differentially expressed by 'RADIATION_THERAPY'

W(pos if higher in 'YES') wilcoxontestP Q AUC
LOC151534|151534 1334 1.375e-06 0.0217 0.7478
CDX1|1044 1359 3.426e-06 0.0217 0.7388
INPP5J|27124 1385 3.474e-06 0.0217 0.7381
KRT18|3875 1430 7.652e-06 0.0271 0.7296
LGALS4|3960 1397 8.471e-06 0.0271 0.7293
ANKS4B|257629 1017 8.715e-06 0.0271 0.7455
TMEM198|130612 1452 1.115e-05 0.0271 0.7255
ALG5|29880 1454 1.153e-05 0.0271 0.7251
DOK7|285489 1464 1.365e-05 0.0276 0.7232
C20ORF134|170487 1477 1.697e-05 0.0276 0.7207
Clinical variable #9: 'KARNOFSKY_PERFORMANCE_SCORE'

30 genes related to 'KARNOFSKY_PERFORMANCE_SCORE'.

Table S16.  Basic characteristics of clinical feature: 'KARNOFSKY_PERFORMANCE_SCORE'

KARNOFSKY_PERFORMANCE_SCORE Mean (SD) 73.58 (16)
  Significant markers N = 30
  pos. correlated 25
  neg. correlated 5
List of top 10 genes differentially expressed by 'KARNOFSKY_PERFORMANCE_SCORE'

Table S17.  Get Full Table List of top 10 genes significantly correlated to 'KARNOFSKY_PERFORMANCE_SCORE' by Spearman correlation test

SpearmanCorr corrP Q
EIF3F|8665 0.5958 1.044e-07 0.00145
EEF1A1P9|441032 0.5894 1.547e-07 0.00145
RPL10A|4736 0.5794 2.791e-07 0.00175
EEA1|8411 -0.5656 6.118e-07 0.00287
MT1F|4494 0.559 8.79e-07 0.00298
SF3B5|83443 0.5575 9.539e-07 0.00298
RPS27A|6233 0.5485 1.542e-06 0.00369
RPS10|6204 0.5482 1.575e-06 0.00369
BBS10|79738 -0.5457 1.787e-06 0.00373
RPL24|6152 0.5307 3.843e-06 0.00721
Clinical variable #10: 'HISTOLOGICAL_TYPE'

30 genes related to 'HISTOLOGICAL_TYPE'.

Table S18.  Basic characteristics of clinical feature: 'HISTOLOGICAL_TYPE'

HISTOLOGICAL_TYPE Labels N
  ESOPHAGUS ADENOCARCINOMA, NOS 89
  ESOPHAGUS SQUAMOUS CELL CARCINOMA 95
     
  Significant markers N = 30
  Higher in ESOPHAGUS SQUAMOUS CELL CARCINOMA 30
  Higher in ESOPHAGUS ADENOCARCINOMA, NOS 0
List of top 10 genes differentially expressed by 'HISTOLOGICAL_TYPE'

Clinical variable #11: 'NUMBER_PACK_YEARS_SMOKED'

30 genes related to 'NUMBER_PACK_YEARS_SMOKED'.

Table S20.  Basic characteristics of clinical feature: 'NUMBER_PACK_YEARS_SMOKED'

NUMBER_PACK_YEARS_SMOKED Mean (SD) 34.72 (22)
  Significant markers N = 30
  pos. correlated 10
  neg. correlated 20
List of top 10 genes differentially expressed by 'NUMBER_PACK_YEARS_SMOKED'

Table S21.  Get Full Table List of top 10 genes significantly correlated to 'NUMBER_PACK_YEARS_SMOKED' by Spearman correlation test

SpearmanCorr corrP Q
SF3B14|51639 -0.4157 2.296e-05 0.138
ZMYND19|116225 -0.4099 3.053e-05 0.138
CCPG1|9236 0.4071 3.506e-05 0.138
NIT2|56954 -0.4054 3.803e-05 0.138
LOC100125556|100125556 -0.4004 4.834e-05 0.138
PCGF1|84759 -0.3912 7.436e-05 0.138
C9ORF6|54942 -0.3883 8.475e-05 0.138
MRPS22|56945 -0.3827 0.0001093 0.138
TPRKB|51002 -0.3822 0.000112 0.138
NOL10|79954 -0.3815 0.0001156 0.138
Clinical variable #12: 'RESIDUAL_TUMOR'

No gene related to 'RESIDUAL_TUMOR'.

Table S22.  Basic characteristics of clinical feature: 'RESIDUAL_TUMOR'

RESIDUAL_TUMOR Labels N
  R0 136
  R1 13
  R2 2
  RX 7
     
  Significant markers N = 0
Clinical variable #13: 'NUMBER_OF_LYMPH_NODES'

No gene related to 'NUMBER_OF_LYMPH_NODES'.

Table S23.  Basic characteristics of clinical feature: 'NUMBER_OF_LYMPH_NODES'

NUMBER_OF_LYMPH_NODES Mean (SD) 2.54 (3.4)
  Significant markers N = 0
Clinical variable #14: 'RACE'

30 genes related to 'RACE'.

Table S24.  Basic characteristics of clinical feature: 'RACE'

RACE Labels N
  ASIAN 46
  BLACK OR AFRICAN AMERICAN 5
  WHITE 113
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'RACE'

Table S25.  Get Full Table List of top 10 genes differentially expressed by 'RACE'

kruskal_wallis_P Q
TMTC3|160418 1.165e-13 2.01e-09
BCL2L1|598 2.853e-13 2.01e-09
LRP12|29967 3.219e-13 2.01e-09
TP63|8626 9.689e-13 4.55e-09
CHODL|140578 1.796e-12 5.21e-09
KCTD15|79047 1.8e-12 5.21e-09
WNT9A|7483 1.942e-12 5.21e-09
RNF217|154214 2.292e-12 5.38e-09
TMC5|79838 4.097e-12 7.82e-09
C3ORF34|84984 4.169e-12 7.82e-09
Clinical variable #15: 'ETHNICITY'

No gene related to 'ETHNICITY'.

Table S26.  Basic characteristics of clinical feature: 'ETHNICITY'

ETHNICITY Labels N
  HISPANIC OR LATINO 5
  NOT HISPANIC OR LATINO 88
     
  Significant markers N = 0
Methods & Data
Input

  • Expresson data file = ESCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

  • Clinical data file = ESCA-TP.merged_data.txt

  • Number of patients = 184

  • Number of genes = 18768

  • Number of clinical features = 15

Selected clinical features

  • Further details on clinical features selected for this analysis, please find a documentation on selected CDEs (Clinical Data Elements). The first column of the file is a formula to convert values and the second column is a clinical parameter name.

  • Survival time data

    • Survival time data is a combined value of days_to_death and days_to_last_followup. For each patient, it creates a combined value 'days_to_death_or_last_fup' using conversion process below.

      • if 'vital_status'==1(dead), 'days_to_last_followup' is always NA. Thus, uses 'days_to_death' value for 'days_to_death_or_fup'

      • if 'vital_status'==0(alive),

        • if 'days_to_death'==NA & 'days_to_last_followup'!=NA, uses 'days_to_last_followup' value for 'days_to_death_or_fup'

        • if 'days_to_death'!=NA, excludes this case in survival analysis and report the case.

      • if 'vital_status'==NA,excludes this case in survival analysis and report the case.

    • cf. In certain diesase types such as SKCM, days_to_death parameter is replaced with time_from_specimen_dx or time_from_specimen_procurement_to_death .

  • This analysis excluded clinical variables that has only NA values.

Survival analysis

For survival clinical features, logrank test in univariate Cox regression analysis with proportional hazards model (Andersen and Gill 1982) was used to estimate the P values comparing quantile intervals using the 'coxph' function in R. Kaplan-Meier survival curves were plotted using quantile intervals at c(0, 0.25, 0.50, 0.75, 1). If there is only one interval group, it will not try survival analysis.

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

Wilcoxon rank sum test (Mann-Whitney U test)

For two groups (mutant or wild-type) of continuous type of clinical data, wilcoxon rank sum test (Mann and Whitney, 1947) was applied to compare their mean difference using 'wilcox.test(continuous.clinical ~ as.factor(group), exact=FALSE)' function in R. This test is equivalent to the Mann-Whitney test.

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] Mann and Whitney, On a Test of Whether one of Two Random Variables is Stochastically Larger than the Other, Annals of Mathematical Statistics 18 (1), 50-60 (1947)
[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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