Correlation between mRNAseq expression and clinical features
Colon Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1K64HFZ
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/C1K64HFZ
Overview
Introduction

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

Summary

Testing the association between 18012 genes and 13 clinical features across 455 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'.

    • PPFIA4|8497 ,  LBX2|85474 ,  ENO3|2027 ,  GABRD|2563 ,  PLA2G12B|84647 ,  ...

  • 30 genes correlated to 'YEARS_TO_BIRTH'.

    • MTERF|7978 ,  MGA|23269 ,  AMH|268 ,  ZNF75A|7627 ,  PPP1R10|5514 ,  ...

  • 30 genes correlated to 'PATHOLOGIC_STAGE'.

    • RGL2|5863 ,  AGPAT5|55326 ,  GSR|2936 ,  NAT1|9 ,  GFI1|2672 ,  ...

  • 30 genes correlated to 'PATHOLOGY_T_STAGE'.

    • RIMKLB|57494 ,  C10ORF114|399726 ,  CSRP2|1466 ,  SOX11|6664 ,  TCHH|7062 ,  ...

  • 30 genes correlated to 'PATHOLOGY_N_STAGE'.

    • AGPAT5|55326 ,  GSR|2936 ,  NAT1|9 ,  PBK|55872 ,  PDE12|201626 ,  ...

  • 30 genes correlated to 'PATHOLOGY_M_STAGE'.

    • LAP3|51056 ,  IRF1|3659 ,  TYMS|7298 ,  GFI1|2672 ,  C13ORF15|28984 ,  ...

  • 5 genes correlated to 'GENDER'.

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

  • 30 genes correlated to 'HISTOLOGICAL_TYPE'.

    • MUC2|4583 ,  PLAGL2|5326 ,  CREB3L1|90993 ,  UQCC|55245 ,  SLC19A3|80704 ,  ...

  • 30 genes correlated to 'RESIDUAL_TUMOR'.

    • LOC150776|150776 ,  SPDYE8P|389517 ,  NSUN5P1|155400 ,  LOC100132287|100132287 ,  LOC100133331|100133331 ,  ...

  • 30 genes correlated to 'NUMBER_OF_LYMPH_NODES'.

    • NPR3|4883 ,  AGPAT5|55326 ,  GSR|2936 ,  NAT1|9 ,  TEAD3|7005 ,  ...

  • 30 genes correlated to 'RACE'.

    • CROCCL1|84809 ,  ULK4|54986 ,  C14ORF167|55449 ,  SPDYE1|285955 ,  LOC441455|441455 ,  ...

  • 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=19 younger N=11
PATHOLOGIC_STAGE Kruskal-Wallis test N=30        
PATHOLOGY_T_STAGE Spearman correlation test N=30 higher stage N=28 lower stage N=2
PATHOLOGY_N_STAGE Spearman correlation test N=30 higher stage N=11 lower stage N=19
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 Wilcoxon test N=30 colon mucinous adenocarcinoma N=30 colon adenocarcinoma N=0
RESIDUAL_TUMOR Kruskal-Wallis test N=30        
NUMBER_OF_LYMPH_NODES Spearman correlation test N=30 higher number_of_lymph_nodes N=10 lower number_of_lymph_nodes N=20
RACE Kruskal-Wallis test N=30        
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=22.2)
  censored N = 353
  death N = 101
     
  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
PPFIA4|8497 1.38e-06 0.025 0.638
LBX2|85474 8.63e-06 0.078 0.618
ENO3|2027 1.31e-05 0.079 0.623
GABRD|2563 2.02e-05 0.091 0.639
PLA2G12B|84647 3.78e-05 0.14 0.494
DCLRE1C|64421 5.62e-05 0.14 0.542
CHDH|55349 7.5e-05 0.14 0.407
PI4K2B|55300 7.62e-05 0.14 0.366
LRRC40|55631 7.84e-05 0.14 0.415
ANKK1|255239 8.56e-05 0.14 0.528
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) 66.95 (13)
  Significant markers N = 30
  pos. correlated 19
  neg. correlated 11
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 -0.2684 7.249e-09 0.000131
MGA|23269 -0.2501 6.914e-08 0.000623
AMH|268 0.2427 2.896e-07 0.00172
ZNF75A|7627 -0.2364 3.819e-07 0.00172
PPP1R10|5514 -0.2313 6.474e-07 0.00233
DNM3|26052 -0.2257 1.216e-06 0.00365
VDAC2|7417 0.2141 4.293e-06 0.00951
LOC154761|154761 0.2139 4.47e-06 0.00951
CNTD2|79935 0.213 5.025e-06 0.00951
TGFBR2|7048 -0.2101 6.46e-06 0.00951
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 74
  STAGE IA 1
  STAGE II 30
  STAGE IIA 137
  STAGE IIB 10
  STAGE IIC 1
  STAGE III 20
  STAGE IIIA 8
  STAGE IIIB 59
  STAGE IIIC 41
  STAGE IV 45
  STAGE IVA 17
  STAGE IVB 2
     
  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
RGL2|5863 8.982e-09 0.000162
AGPAT5|55326 1.572e-07 0.0012
GSR|2936 1.99e-07 0.0012
NAT1|9 3.954e-07 0.00144
GFI1|2672 4.329e-07 0.00144
C5ORF23|79614 5.33e-07 0.00144
TEAD3|7005 5.606e-07 0.00144
PBK|55872 6.88e-07 0.00155
ESCO2|157570 1.566e-06 0.00293
CDCA2|157313 1.624e-06 0.00293
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) 2.91 (0.62)
  N
  T1 11
  T2 77
  T3 310
  T4 56
     
  Significant markers N = 30
  pos. correlated 28
  neg. correlated 2
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
RIMKLB|57494 0.2319 5.836e-07 0.00844
C10ORF114|399726 0.2284 1.147e-06 0.00844
CSRP2|1466 0.2241 1.406e-06 0.00844
SOX11|6664 0.2247 1.982e-06 0.00893
TCHH|7062 0.223 3.191e-06 0.00902
FSTL3|10272 0.2148 3.854e-06 0.00902
RBP7|116362 0.2143 4.595e-06 0.00902
C11ORF41|25758 0.2139 4.692e-06 0.00902
CAMK2B|816 0.2273 5.034e-06 0.00902
C5ORF23|79614 0.2158 5.18e-06 0.00902
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) 0.59 (0.78)
  N
  N0 268
  N1 105
  N2 82
     
  Significant markers N = 30
  pos. correlated 11
  neg. correlated 19
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
AGPAT5|55326 -0.3157 5.507e-12 9.92e-08
GSR|2936 -0.3075 2.014e-11 1.81e-07
NAT1|9 -0.3032 3.973e-11 2.39e-07
PBK|55872 -0.295 1.437e-10 6.47e-07
PDE12|201626 -0.2901 2.856e-10 9.12e-07
NPR3|4883 0.3119 3.038e-10 9.12e-07
INTS10|55174 -0.2856 5.505e-10 1.4e-06
ESCO2|157570 -0.2845 6.949e-10 1.4e-06
TEAD3|7005 0.2839 7.004e-10 1.4e-06
CDCA2|157313 -0.2813 1.049e-09 1.89e-06
Clinical variable #6: 'PATHOLOGY_M_STAGE'

30 genes related to 'PATHOLOGY_M_STAGE'.

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

PATHOLOGY_M_STAGE Labels N
  class0 334
  class1 64
     
  Significant markers N = 30
  Higher in class1 30
  Higher in class0 0
List of top 10 genes differentially expressed by 'PATHOLOGY_M_STAGE'

Table S12.  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 5423 4.251e-10 7.66e-06 0.7463
IRF1|3659 6192 9.695e-08 0.000873 0.7103
TYMS|7298 6264 1.546e-07 0.000928 0.707
GFI1|2672 6343 2.56e-07 0.00115 0.7033
C13ORF15|28984 14947 4.39e-07 0.00142 0.6992
HOXA4|3201 14848 4.718e-07 0.00142 0.6988
CXCL9|4283 6487 6.279e-07 0.00147 0.6965
CXCR6|10663 6489 7.206e-07 0.00147 0.6955
ZSCAN5A|79149 6513 7.361e-07 0.00147 0.6953
RASGRP1|10125 6542 1.127e-06 0.00203 0.6921
Clinical variable #7: 'GENDER'

5 genes related to 'GENDER'.

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

GENDER Labels N
  FEMALE 215
  MALE 240
     
  Significant markers N = 5
  Higher in MALE 5
  Higher in FEMALE 0
List of 5 genes differentially expressed by 'GENDER'

Table S14.  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 13550 1.155e-30 2.08e-27 0.9905
CYORF15B|84663 10949 3.318e-25 3.98e-22 0.9788
CA5BP|340591 12044 8.932e-23 1.01e-19 0.7666
HDHD1A|8226 12299 5.353e-22 5.67e-19 0.7616
NCRNA00183|554203 14374 3.367e-16 2.72e-13 0.7214
Clinical variable #8: 'RADIATION_THERAPY'

No gene related to 'RADIATION_THERAPY'.

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

RADIATION_THERAPY Labels N
  NO 377
  YES 9
     
  Significant markers N = 0
Clinical variable #9: 'HISTOLOGICAL_TYPE'

30 genes related to 'HISTOLOGICAL_TYPE'.

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

HISTOLOGICAL_TYPE Labels N
  COLON ADENOCARCINOMA 388
  COLON MUCINOUS ADENOCARCINOMA 62
     
  Significant markers N = 30
  Higher in COLON MUCINOUS ADENOCARCINOMA 30
  Higher in COLON ADENOCARCINOMA 0
List of top 10 genes differentially expressed by 'HISTOLOGICAL_TYPE'

Table S17.  Get Full Table List of top 10 genes differentially expressed by 'HISTOLOGICAL_TYPE'

W(pos if higher in 'COLON MUCINOUS ADENOCARCINOMA') wilcoxontestP Q AUC
MUC2|4583 19853 1.888e-16 3.4e-12 0.8253
PLAGL2|5326 4427 1.312e-15 1.18e-11 0.816
CREB3L1|90993 19429 7.078e-15 3.51e-11 0.8077
UQCC|55245 4658 9.154e-15 3.51e-11 0.8064
SLC19A3|80704 4665.5 9.741e-15 3.51e-11 0.8061
TAF4|6874 4795 2.818e-14 8.23e-11 0.8007
SLC5A6|8884 4824 3.566e-14 8.23e-11 0.7995
TOMM34|10953 4827 3.654e-14 8.23e-11 0.7993
AQP3|360 19152 6.795e-14 1.36e-10 0.7961
SPDEF|25803 19125 8.434e-14 1.52e-10 0.795
Clinical variable #10: 'RESIDUAL_TUMOR'

30 genes related to 'RESIDUAL_TUMOR'.

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

RESIDUAL_TUMOR Labels N
  R0 329
  R1 4
  R2 24
  RX 25
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'RESIDUAL_TUMOR'

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

kruskal_wallis_P Q
LOC150776|150776 1.559e-10 1.06e-06
SPDYE8P|389517 1.884e-10 1.06e-06
NSUN5P1|155400 2.08e-10 1.06e-06
LOC100132287|100132287 2.407e-10 1.06e-06
LOC100133331|100133331 2.945e-10 1.06e-06
RRN3P2|653390 4.394e-10 1.32e-06
POLR2J4|84820 1.148e-09 2.78e-06
RRP7B|91695 1.236e-09 2.78e-06
LOC339047|339047 1.606e-09 3.21e-06
RPL36A|6173 2.166e-09 3.29e-06
Clinical variable #11: 'NUMBER_OF_LYMPH_NODES'

30 genes related to 'NUMBER_OF_LYMPH_NODES'.

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

NUMBER_OF_LYMPH_NODES Mean (SD) 2.05 (4.4)
  Significant markers N = 30
  pos. correlated 10
  neg. correlated 20
List of top 10 genes differentially expressed by 'NUMBER_OF_LYMPH_NODES'

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

SpearmanCorr corrP Q
NPR3|4883 0.3258 1.504e-10 1.94e-06
AGPAT5|55326 -0.2994 2.356e-10 1.94e-06
GSR|2936 -0.2972 3.238e-10 1.94e-06
NAT1|9 -0.2844 1.912e-09 8.61e-06
TEAD3|7005 0.2789 4.016e-09 1.31e-05
RGL2|5863 0.2774 4.925e-09 1.31e-05
C5ORF23|79614 0.2822 5.11e-09 1.31e-05
PBK|55872 -0.2745 7.444e-09 1.68e-05
INTS10|55174 -0.2725 9.279e-09 1.86e-05
MINPP1|9562 -0.27 1.276e-08 2.3e-05
Clinical variable #12: 'RACE'

30 genes related to 'RACE'.

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

RACE Labels N
  AMERICAN INDIAN OR ALASKA NATIVE 1
  ASIAN 11
  BLACK OR AFRICAN AMERICAN 59
  WHITE 213
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'RACE'

Table S23.  Get Full Table List of top 10 genes differentially expressed by 'RACE'

kruskal_wallis_P Q
CROCCL1|84809 3.386e-13 6.1e-09
ULK4|54986 1.272e-12 1.15e-08
C14ORF167|55449 1.976e-12 1.19e-08
SPDYE1|285955 3.867e-10 1.74e-06
LOC441455|441455 6.017e-10 2.17e-06
SPDYE6|729597 8.632e-10 2.59e-06
LOC100190986|100190986 2.111e-09 5.43e-06
SPDYE5|442590 6.836e-09 1.54e-05
BCO2|83875 8.447e-09 1.56e-05
?|645851 9.024e-09 1.56e-05
Clinical variable #13: 'ETHNICITY'

No gene related to 'ETHNICITY'.

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

ETHNICITY Labels N
  HISPANIC OR LATINO 4
  NOT HISPANIC OR LATINO 270
     
  Significant markers N = 0
Methods & Data
Input

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

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

  • Number of patients = 455

  • Number of genes = 18012

  • 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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