Correlation between mRNAseq expression and clinical features
Colorectal Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1RJ4HTW
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/C1RJ4HTW
Overview
Introduction

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

Summary

Testing the association between 18041 genes and 13 clinical features across 621 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 11 clinical features related to at least one genes.

  • 30 genes correlated to 'DAYS_TO_DEATH_OR_LAST_FUP'.

    • GABRD|2563 ,  LOC220930|220930 ,  GTF2A1L|11036 ,  PLA2G12B|84647 ,  ENO3|2027 ,  ...

  • 30 genes correlated to 'YEARS_TO_BIRTH'.

    • MTERF|7978 ,  MGA|23269 ,  AMH|268 ,  ZNF75A|7627 ,  CNTD2|79935 ,  ...

  • 30 genes correlated to 'TUMOR_TISSUE_SITE'.

    • HOXB13|10481 ,  ZNF528|84436 ,  ELAVL2|1993 ,  HOXC6|3223 ,  HOXC4|3221 ,  ...

  • 30 genes correlated to 'PATHOLOGIC_STAGE'.

    • RGL2|5863 ,  GSR|2936 ,  C5ORF23|79614 ,  GFI1|2672 ,  TEAD3|7005 ,  ...

  • 30 genes correlated to 'PATHOLOGY_T_STAGE'.

    • SCG2|7857 ,  C5ORF23|79614 ,  CSRP2|1466 ,  RBP7|116362 ,  SOX11|6664 ,  ...

  • 30 genes correlated to 'PATHOLOGY_N_STAGE'.

    • GSR|2936 ,  TEAD3|7005 ,  C5ORF23|79614 ,  AGPAT5|55326 ,  NPR3|4883 ,  ...

  • 30 genes correlated to 'PATHOLOGY_M_STAGE'.

    • LAP3|51056 ,  IRF1|3659 ,  GFI1|2672 ,  C13ORF15|28984 ,  CIITA|4261 ,  ...

  • 5 genes correlated to 'GENDER'.

    • CYORF15A|246126 ,  CYORF15B|84663 ,  HDHD1A|8226 ,  CA5BP|340591 ,  NCRNA00183|554203

  • 30 genes correlated to 'HISTOLOGICAL_TYPE'.

    • PLAGL2|5326 ,  POFUT1|23509 ,  MUC2|4583 ,  TAF4|6874 ,  SPDEF|25803 ,  ...

  • 30 genes correlated to 'RESIDUAL_TUMOR'.

    • LOC150776|150776 ,  RRN3P2|653390 ,  PMS2CL|441194 ,  SPDYE8P|389517 ,  POLR2J4|84820 ,  ...

  • 30 genes correlated to 'NUMBER_OF_LYMPH_NODES'.

    • GSR|2936 ,  C5ORF23|79614 ,  NPR3|4883 ,  TEAD3|7005 ,  AGPAT5|55326 ,  ...

  • No genes correlated to 'RADIATION_THERAPY', 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=30   N=NA   N=NA
YEARS_TO_BIRTH Spearman correlation test N=30 older N=12 younger N=18
TUMOR_TISSUE_SITE Wilcoxon test N=30 rectum N=30 colon N=0
PATHOLOGIC_STAGE Kruskal-Wallis test N=30        
PATHOLOGY_T_STAGE Spearman correlation test N=30 higher stage N=27 lower stage N=3
PATHOLOGY_N_STAGE Spearman correlation test N=30 higher stage N=12 lower stage N=18
PATHOLOGY_M_STAGE Wilcoxon test N=30 class1 N=30 class0 N=0
GENDER Wilcoxon test N=5 male N=5 female N=0
RADIATION_THERAPY Wilcoxon test   N=0        
HISTOLOGICAL_TYPE Kruskal-Wallis test N=30        
RESIDUAL_TUMOR Kruskal-Wallis test N=30        
NUMBER_OF_LYMPH_NODES Spearman correlation test N=30 higher number_of_lymph_nodes N=12 lower number_of_lymph_nodes N=18
ETHNICITY Wilcoxon test   N=0        
Clinical variable #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

30 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) 0-148 (median=22.1)
  censored N = 492
  death N = 128
     
  Significant markers N = 30
  associated with shorter survival NA
  associated with longer survival NA
List of top 10 genes differentially expressed by 'DAYS_TO_DEATH_OR_LAST_FUP'

Table S2.  Get Full Table List of top 10 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
GABRD|2563 9.98e-07 0.018 0.625
LOC220930|220930 5.31e-06 0.048 0.595
GTF2A1L|11036 1.18e-05 0.06 0.615
PLA2G12B|84647 1.43e-05 0.06 0.486
ENO3|2027 1.99e-05 0.06 0.613
HOXC6|3223 1.99e-05 0.06 0.652
DPP7|29952 2.53e-05 0.063 0.627
TRDMT1|1787 3.5e-05 0.063 0.443
GNG10|2790 3.71e-05 0.063 0.533
PI4K2B|55300 3.96e-05 0.063 0.379
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) 66.33 (13)
  Significant markers N = 30
  pos. correlated 12
  neg. correlated 18
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
MTERF|7978 -0.2431 9.744e-10 1.19e-05
MGA|23269 -0.2407 1.322e-09 1.19e-05
AMH|268 0.2267 2.141e-08 0.000129
ZNF75A|7627 -0.2078 1.906e-07 0.000859
CNTD2|79935 0.206 2.437e-07 0.000879
LOC154761|154761 0.1997 5.604e-07 0.00151
PPP1R10|5514 -0.1992 5.872e-07 0.00151
TGFBR2|7048 -0.1946 1.074e-06 0.00216
MRE11A|4361 -0.1944 1.116e-06 0.00216
ZNF518B|85460 -0.194 1.2e-06 0.00216
Clinical variable #3: 'TUMOR_TISSUE_SITE'

30 genes related to 'TUMOR_TISSUE_SITE'.

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

TUMOR_TISSUE_SITE Labels N
  COLON 454
  RECTUM 163
     
  Significant markers N = 30
  Higher in RECTUM 30
  Higher in COLON 0
List of top 10 genes differentially expressed by 'TUMOR_TISSUE_SITE'

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

W(pos if higher in 'RECTUM') wilcoxontestP Q AUC
HOXB13|10481 52154 3.399e-15 6.13e-11 0.7079
ZNF528|84436 49224.5 1.903e-10 1.72e-06 0.6681
ELAVL2|1993 40271 3.857e-10 1.86e-06 0.6715
HOXC6|3223 16185 4.117e-10 1.86e-06 0.6838
HOXC4|3221 19461.5 5.611e-10 2.02e-06 0.6736
ZNF813|126017 48508 1.01e-09 3.04e-06 0.6613
ZNF662|389114 48413 1.372e-09 3.54e-06 0.66
ZNF530|348327 48481 2.142e-09 4.83e-06 0.658
ZNF141|7700 48042 3.206e-09 6.03e-06 0.6564
MAP7D2|256714 46936 3.341e-09 6.03e-06 0.657
Clinical variable #4: 'PATHOLOGIC_STAGE'

30 genes related to 'PATHOLOGIC_STAGE'.

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

PATHOLOGIC_STAGE Labels N
  STAGE I 104
  STAGE IA 1
  STAGE II 38
  STAGE IIA 177
  STAGE IIB 12
  STAGE IIC 2
  STAGE III 25
  STAGE IIIA 15
  STAGE IIIB 84
  STAGE IIIC 55
  STAGE IV 62
  STAGE IVA 24
  STAGE IVB 2
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'PATHOLOGIC_STAGE'

Table S8.  Get Full Table List of top 10 genes differentially expressed by 'PATHOLOGIC_STAGE'

kruskal_wallis_P Q
RGL2|5863 1.893e-09 2.76e-05
GSR|2936 3.062e-09 2.76e-05
C5ORF23|79614 1.046e-08 6.29e-05
GFI1|2672 5.956e-08 0.000233
TEAD3|7005 7.168e-08 0.000233
C13ORF15|28984 9.567e-08 0.000233
CFDP1|10428 1.106e-07 0.000233
C2CD4A|145741 1.161e-07 0.000233
CASP1|834 1.201e-07 0.000233
TMEM55A|55529 1.291e-07 0.000233
Clinical variable #5: 'PATHOLOGY_T_STAGE'

30 genes related to 'PATHOLOGY_T_STAGE'.

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

PATHOLOGY_T_STAGE Mean (SD) 2.88 (0.63)
  N
  T1 20
  T2 105
  T3 423
  T4 70
     
  Significant markers N = 30
  pos. correlated 27
  neg. correlated 3
List of top 10 genes differentially expressed by 'PATHOLOGY_T_STAGE'

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

SpearmanCorr corrP Q
SCG2|7857 0.2591 7.327e-11 1.32e-06
C5ORF23|79614 0.2469 1.106e-09 9.98e-06
CSRP2|1466 0.237 2.436e-09 1.3e-05
RBP7|116362 0.2369 2.893e-09 1.3e-05
SOX11|6664 0.2364 4.854e-09 1.75e-05
NALCN|259232 0.2434 9.139e-09 2.1e-05
SPP1|6696 0.2283 9.42e-09 2.1e-05
RIMKLB|57494 0.2275 1.064e-08 2.1e-05
LOC100126784|100126784 0.2405 1.161e-08 2.1e-05
CDH2|1000 0.2286 1.41e-08 2.1e-05
Clinical variable #6: 'PATHOLOGY_N_STAGE'

30 genes related to 'PATHOLOGY_N_STAGE'.

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

PATHOLOGY_N_STAGE Mean (SD) 0.62 (0.78)
  N
  N0 352
  N1 150
  N2 115
     
  Significant markers N = 30
  pos. correlated 12
  neg. correlated 18
List of top 10 genes differentially expressed by 'PATHOLOGY_N_STAGE'

Table S12.  Get Full Table List of top 10 genes significantly correlated to 'PATHOLOGY_N_STAGE' by Spearman correlation test

SpearmanCorr corrP Q
GSR|2936 -0.2904 1.883e-13 3.4e-09
TEAD3|7005 0.2704 8.48e-12 7.65e-08
C5ORF23|79614 0.2668 4.182e-11 2.51e-07
AGPAT5|55326 -0.2591 6.356e-11 2.87e-07
NPR3|4883 0.2721 2.129e-10 7.68e-07
COQ2|27235 -0.2505 2.773e-10 8.34e-07
NAT1|9 -0.2486 3.827e-10 9.86e-07
RGL2|5863 0.2449 7.059e-10 1.59e-06
PBK|55872 -0.2398 1.674e-09 3.36e-06
CASP1|834 -0.2381 2.127e-09 3.84e-06
Clinical variable #7: 'PATHOLOGY_M_STAGE'

30 genes related to 'PATHOLOGY_M_STAGE'.

Table S13.  Basic characteristics of clinical feature: 'PATHOLOGY_M_STAGE'

PATHOLOGY_M_STAGE Labels N
  class0 460
  class1 87
     
  Significant markers N = 30
  Higher in class1 30
  Higher in class0 0
List of top 10 genes differentially expressed by 'PATHOLOGY_M_STAGE'

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

W(pos if higher in 'class1') wilcoxontestP Q AUC
LAP3|51056 11575 4.401e-10 7.94e-06 0.7108
IRF1|3659 12372 1.609e-08 0.000145 0.6909
GFI1|2672 12644 5.084e-08 0.000306 0.6841
C13ORF15|28984 27118 1.46e-07 0.000659 0.6776
CIITA|4261 13036 2.491e-07 0.000782 0.6743
WARS|7453 13047 2.602e-07 0.000782 0.674
RARRES3|5920 13102 3.229e-07 0.000832 0.6726
IDO1|3620 13098 4.011e-07 0.000905 0.6713
TYMS|7298 13235 5.41e-07 0.00108 0.6693
FASLG|356 12294.5 8.365e-07 0.00151 0.6701
Clinical variable #8: 'GENDER'

5 genes related to 'GENDER'.

Table S15.  Basic characteristics of clinical feature: 'GENDER'

GENDER Labels N
  FEMALE 290
  MALE 331
     
  Significant markers N = 5
  Higher in MALE 5
  Higher in FEMALE 0
List of 5 genes differentially expressed by 'GENDER'

Table S16.  Get Full Table List of 5 genes differentially expressed by 'GENDER'. 25 significant gene(s) located in sex chromosomes is(are) filtered out.

W(pos if higher in 'MALE') wilcoxontestP Q AUC
CYORF15A|246126 24807 6.508e-40 1.3e-36 0.9861
CYORF15B|84663 21563 5.274e-35 6.8e-32 0.9782
HDHD1A|8226 22584 4.589e-30 5.17e-27 0.7647
CA5BP|340591 23916 3.645e-27 3.65e-24 0.7508
NCRNA00183|554203 25892 3.81e-23 3.12e-20 0.7303
Clinical variable #9: 'RADIATION_THERAPY'

No gene related to 'RADIATION_THERAPY'.

Table S17.  Basic characteristics of clinical feature: 'RADIATION_THERAPY'

RADIATION_THERAPY Labels N
  NO 489
  YES 30
     
  Significant markers N = 0
Clinical variable #10: 'HISTOLOGICAL_TYPE'

30 genes related to 'HISTOLOGICAL_TYPE'.

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

HISTOLOGICAL_TYPE Labels N
  COLON ADENOCARCINOMA 388
  COLON MUCINOUS ADENOCARCINOMA 62
  RECTAL ADENOCARCINOMA 147
  RECTAL MUCINOUS ADENOCARCINOMA 13
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'HISTOLOGICAL_TYPE'

Table S19.  Get Full Table List of top 10 genes differentially expressed by 'HISTOLOGICAL_TYPE'

kruskal_wallis_P Q
PLAGL2|5326 2.475e-21 4.47e-17
POFUT1|23509 2.964e-20 2.67e-16
MUC2|4583 1.455e-19 8.75e-16
TAF4|6874 3.694e-19 1.67e-15
SPDEF|25803 6.69e-19 2.37e-15
SLC5A6|8884 7.896e-19 2.37e-15
KIAA0406|9675 9.233e-19 2.38e-15
SNHG11|128439 1.405e-18 3.17e-15
SLC19A3|80704 1.733e-18 3.36e-15
TOMM34|10953 1.863e-18 3.36e-15
Clinical variable #11: 'RESIDUAL_TUMOR'

30 genes related to 'RESIDUAL_TUMOR'.

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

RESIDUAL_TUMOR Labels N
  R0 452
  R1 6
  R2 36
  RX 30
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'RESIDUAL_TUMOR'

Table S21.  Get Full Table List of top 10 genes differentially expressed by 'RESIDUAL_TUMOR'

kruskal_wallis_P Q
LOC150776|150776 4.021e-12 6.51e-08
RRN3P2|653390 8.89e-12 6.51e-08
PMS2CL|441194 1.566e-11 6.51e-08
SPDYE8P|389517 1.623e-11 6.51e-08
POLR2J4|84820 1.804e-11 6.51e-08
NSUN5P1|155400 3.608e-11 1.06e-07
GUSBL2|375513 4.138e-11 1.06e-07
AGAP11|119385 5.593e-11 1.06e-07
GUSBL1|387036 5.746e-11 1.06e-07
STAG3L2|442582 5.879e-11 1.06e-07
Clinical variable #12: 'NUMBER_OF_LYMPH_NODES'

30 genes related to 'NUMBER_OF_LYMPH_NODES'.

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

NUMBER_OF_LYMPH_NODES Mean (SD) 2.22 (4.7)
  Significant markers N = 30
  pos. correlated 12
  neg. correlated 18
List of top 10 genes differentially expressed by 'NUMBER_OF_LYMPH_NODES'

Table S23.  Get Full Table List of top 10 genes significantly correlated to 'NUMBER_OF_LYMPH_NODES' by Spearman correlation test

SpearmanCorr corrP Q
GSR|2936 -0.2821 3.517e-12 6.35e-08
C5ORF23|79614 0.2686 9.938e-11 8.96e-07
NPR3|4883 0.2795 1.913e-10 1.15e-06
TEAD3|7005 0.2531 5.117e-10 2.31e-06
AGPAT5|55326 -0.2502 8.18e-10 2.95e-06
CASP1|834 -0.2471 1.331e-09 4e-06
CXCL2|2920 -0.2443 2.069e-09 5.33e-06
COQ2|27235 -0.241 3.424e-09 6.88e-06
TCHH|7062 0.2472 3.596e-09 6.88e-06
SHC1|6464 0.2403 3.812e-09 6.88e-06
Clinical variable #13: 'ETHNICITY'

No gene related to 'ETHNICITY'.

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

ETHNICITY Labels N
  HISPANIC OR LATINO 5
  NOT HISPANIC OR LATINO 352
     
  Significant markers N = 0
Methods & Data
Input

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

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

  • Number of patients = 621

  • Number of genes = 18041

  • Number of clinical features = 13

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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