Correlation between mRNAseq expression and clinical features
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
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/C18P5ZWK
Overview
Introduction

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

Summary

Testing the association between 18278 genes and 12 clinical features across 533 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 9 clinical features related to at least one genes.

  • 30 genes correlated to 'DAYS_TO_DEATH_OR_LAST_FUP'.

    • C15ORF42|90381 ,  CCNF|899 ,  DONSON|29980 ,  DVL3|1857 ,  POFUT2|23275 ,  ...

  • 30 genes correlated to 'YEARS_TO_BIRTH'.

    • RANBP17|64901 ,  RFPL1S|10740 ,  UTY|7404 ,  WFDC1|58189 ,  NEFH|4744 ,  ...

  • 30 genes correlated to 'PATHOLOGIC_STAGE'.

    • PLEKHA9|51054 ,  NR3C2|4306 ,  IL20RB|53833 ,  ZNF132|7691 ,  FKBP11|51303 ,  ...

  • 30 genes correlated to 'PATHOLOGY_T_STAGE'.

    • ZNF132|7691 ,  PLEKHA9|51054 ,  NR3C2|4306 ,  FKBP11|51303 ,  SHOX2|6474 ,  ...

  • 30 genes correlated to 'PATHOLOGY_N_STAGE'.

    • CDCA8|55143 ,  FAM64A|54478 ,  PI3|5266 ,  RHBDF2|79651 ,  PLK1|5347 ,  ...

  • 30 genes correlated to 'PATHOLOGY_M_STAGE'.

    • PLEKHA9|51054 ,  IL20RB|53833 ,  GARNL3|84253 ,  INHBE|83729 ,  C22ORF9|23313 ,  ...

  • 9 genes correlated to 'GENDER'.

    • NCRNA00183|554203 ,  HDHD1A|8226 ,  DNAJB13|374407 ,  RAB42|115273 ,  RERG|85004 ,  ...

  • 7 genes correlated to 'KARNOFSKY_PERFORMANCE_SCORE'.

    • NCL|4691 ,  LOC100271831|100271831 ,  RIOK2|55781 ,  SMARCC2|6601 ,  DKC1|1736 ,  ...

  • 30 genes correlated to 'RACE'.

    • TUBB8|347688 ,  LOC90784|90784 ,  NOTCH2NL|388677 ,  PWWP2B|170394 ,  DHX30|22907 ,  ...

  • No genes correlated to 'NUMBER_PACK_YEARS_SMOKED', 'YEAR_OF_TOBACCO_SMOKING_ONSET', 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=5 younger N=25
PATHOLOGIC_STAGE Kruskal-Wallis test N=30        
PATHOLOGY_T_STAGE Spearman correlation test N=30 higher stage N=16 lower stage N=14
PATHOLOGY_N_STAGE Wilcoxon test N=30 n1 N=30 n0 N=0
PATHOLOGY_M_STAGE Wilcoxon test N=30 class1 N=30 class0 N=0
GENDER Wilcoxon test N=9 male N=9 female N=0
KARNOFSKY_PERFORMANCE_SCORE Spearman correlation test N=7 higher score N=5 lower score N=2
NUMBER_PACK_YEARS_SMOKED Spearman correlation test   N=0        
YEAR_OF_TOBACCO_SMOKING_ONSET 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'

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) 0.1-149.2 (median=39.3)
  censored N = 357
  death N = 175
     
  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
C15ORF42|90381 0 0 0.662
CCNF|899 0 0 0.669
DONSON|29980 0 0 0.692
DVL3|1857 0 0 0.663
POFUT2|23275 0 0 0.656
CORO6|84940 1.11e-16 2.3e-13 0.649
KIF18B|146909 1.11e-16 2.3e-13 0.663
SUV420H2|84787 1.11e-16 2.3e-13 0.629
ZNF26|7574 1.11e-16 2.3e-13 0.645
ARFGAP1|55738 2.22e-16 3.4e-13 0.67
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) 60.6 (12)
  Significant markers N = 30
  pos. correlated 5
  neg. correlated 25
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
RANBP17|64901 -0.2625 7.86e-10 1.44e-05
RFPL1S|10740 -0.2595 1.594e-09 1.46e-05
UTY|7404 -0.2894 4.239e-09 2.29e-05
WFDC1|58189 -0.25 5.018e-09 2.29e-05
NEFH|4744 -0.2466 8.255e-09 3.02e-05
PALLD|23022 -0.2343 4.569e-08 0.000139
KDM5D|8284 -0.2572 7.008e-08 0.000183
NDUFAF2|91942 0.2298 8.308e-08 0.00019
USP9Y|8287 -0.2574 9.808e-08 0.000199
ZFY|7544 -0.2461 1.126e-07 0.000206
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 267
  STAGE II 57
  STAGE III 123
  STAGE IV 84
     
  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
PLEKHA9|51054 3.933e-19 7.19e-15
NR3C2|4306 8.937e-17 8.17e-13
IL20RB|53833 2.205e-16 1.34e-12
ZNF132|7691 6.989e-16 3.19e-12
FKBP11|51303 1.794e-15 6.56e-12
TRIM36|55521 2.397e-15 7.29e-12
BIRC5|332 3.585e-15 7.29e-12
NFE2L3|9603 3.83e-15 7.29e-12
NOP2|4839 3.898e-15 7.29e-12
INHBE|83729 3.99e-15 7.29e-12
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) 1.87 (0.96)
  N
  T1 273
  T2 69
  T3 180
  T4 11
     
  Significant markers N = 30
  pos. correlated 16
  neg. correlated 14
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
ZNF132|7691 -0.3697 1.058e-18 1.55e-14
PLEKHA9|51054 0.3676 1.7e-18 1.55e-14
NR3C2|4306 -0.3647 3.272e-18 1.99e-14
FKBP11|51303 0.3498 8.629e-17 3.94e-13
SHOX2|6474 0.3474 5.732e-16 2.1e-12
TRIM36|55521 0.3388 8.73e-16 2.41e-12
CAPZA1|829 0.3386 9.246e-16 2.41e-12
TMEM150C|441027 -0.3373 1.2e-15 2.74e-12
RBCK1|10616 0.3363 1.461e-15 2.81e-12
ANKRD56|345079 -0.3367 1.54e-15 2.81e-12
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 Labels N
  N0 240
  N1 16
     
  Significant markers N = 30
  Higher in N1 30
  Higher in N0 0
List of top 10 genes differentially expressed by 'PATHOLOGY_N_STAGE'

Table S10.  Get Full Table List of top 10 genes differentially expressed by 'PATHOLOGY_N_STAGE'

W(pos if higher in 'N1') wilcoxontestP Q AUC
CDCA8|55143 3342.5 7.101e-07 0.00588 0.8704
FAM64A|54478 3306 1.067e-06 0.00588 0.8645
PI3|5266 2772 1.178e-06 0.00588 0.8758
RHBDF2|79651 3309 1.287e-06 0.00588 0.8617
PLK1|5347 3296 1.615e-06 0.0059 0.8583
CEP55|55165 3274 2.362e-06 0.00609 0.8526
UBE2T|29089 3265 2.754e-06 0.00609 0.8503
GRB2|2885 3262 2.899e-06 0.00609 0.8495
FOXM1|2305 3252 3.434e-06 0.00609 0.8469
SKA1|220134 3250 3.552e-06 0.00609 0.8464
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 422
  class1 79
     
  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
PLEKHA9|51054 24695 1.077e-11 1.97e-07 0.7407
IL20RB|53833 24533.5 2.756e-11 2.16e-07 0.7359
GARNL3|84253 8848 3.538e-11 2.16e-07 0.7346
INHBE|83729 24223 8.508e-11 3.34e-07 0.73
C22ORF9|23313 24266 1.255e-10 3.34e-07 0.7279
SKA1|220134 24215 1.666e-10 3.34e-07 0.7263
BIRC5|332 24208 1.732e-10 3.34e-07 0.7261
ENPP5|59084 9133 1.761e-10 3.34e-07 0.726
UBE2C|11065 24184 1.977e-10 3.34e-07 0.7254
GTSE1|51512 24127 1.989e-10 3.34e-07 0.7254
Clinical variable #7: 'GENDER'

9 genes related to 'GENDER'.

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

GENDER Labels N
  FEMALE 188
  MALE 345
     
  Significant markers N = 9
  Higher in MALE 9
  Higher in FEMALE 0
List of 9 genes differentially expressed by 'GENDER'

Table S14.  Get Full Table List of 9 genes differentially expressed by 'GENDER'. 21 significant gene(s) located in sex chromosomes is(are) filtered out.

W(pos if higher in 'MALE') wilcoxontestP Q AUC
NCRNA00183|554203 8419 2.38e-45 4.83e-42 0.8702
HDHD1A|8226 10723.5 2.219e-37 3.12e-34 0.8347
DNAJB13|374407 48907 6.419e-32 7.33e-29 0.8151
RAB42|115273 51867 2.62e-30 2.66e-27 0.7997
RERG|85004 49947 6.319e-25 4.81e-22 0.7701
CYORF15A|246126 14952 2.78e-24 2.03e-21 0.9659
RNASET2|8635 49307 2.968e-23 2.01e-20 0.7602
CYORF15B|84663 13651 1.595e-21 1.01e-18 0.9504
CDHR1|92211 48190 4.025e-21 2.45e-18 0.7473
Clinical variable #8: 'KARNOFSKY_PERFORMANCE_SCORE'

7 genes related to 'KARNOFSKY_PERFORMANCE_SCORE'.

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

KARNOFSKY_PERFORMANCE_SCORE Mean (SD) 87.17 (23)
  Significant markers N = 7
  pos. correlated 5
  neg. correlated 2
List of 7 genes differentially expressed by 'KARNOFSKY_PERFORMANCE_SCORE'

Table S16.  Get Full Table List of 7 genes significantly correlated to 'KARNOFSKY_PERFORMANCE_SCORE' by Spearman correlation test

SpearmanCorr corrP Q
NCL|4691 0.5844 4.338e-06 0.0793
LOC100271831|100271831 -0.7194 2.349e-05 0.196
RIOK2|55781 0.5383 3.223e-05 0.196
SMARCC2|6601 -0.5134 8.439e-05 0.282
DKC1|1736 0.51 9.567e-05 0.282
UTP14A|10813 0.5082 0.0001023 0.282
CLP1|10978 0.5068 0.000108 0.282
Clinical variable #9: 'NUMBER_PACK_YEARS_SMOKED'

No gene related to 'NUMBER_PACK_YEARS_SMOKED'.

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

NUMBER_PACK_YEARS_SMOKED Mean (SD) 28.33 (16)
  Significant markers N = 0
Clinical variable #10: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

No gene related to 'YEAR_OF_TOBACCO_SMOKING_ONSET'.

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

YEAR_OF_TOBACCO_SMOKING_ONSET Mean (SD) 1979.25 (18)
  Significant markers N = 0
Clinical variable #11: 'RACE'

30 genes related to 'RACE'.

Table S19.  Basic characteristics of clinical feature: 'RACE'

RACE Labels N
  ASIAN 8
  BLACK OR AFRICAN AMERICAN 56
  WHITE 462
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'RACE'

Table S20.  Get Full Table List of top 10 genes differentially expressed by 'RACE'

kruskal_wallis_P Q
TUBB8|347688 1.918e-15 3.51e-11
LOC90784|90784 4.548e-13 4.16e-09
NOTCH2NL|388677 8.582e-13 5.23e-09
PWWP2B|170394 5.708e-12 2.61e-08
DHX30|22907 8.809e-12 3.05e-08
NACA2|342538 1.002e-11 3.05e-08
FAM114A1|92689 2.368e-11 6.18e-08
ANKRD9|122416 5.214e-11 1.1e-07
FTHL3|2498 5.407e-11 1.1e-07
MTMR2|8898 1.222e-10 2.23e-07
Clinical variable #12: 'ETHNICITY'

No gene related to 'ETHNICITY'.

Table S21.  Basic characteristics of clinical feature: 'ETHNICITY'

ETHNICITY Labels N
  HISPANIC OR LATINO 26
  NOT HISPANIC OR LATINO 355
     
  Significant markers N = 0
Methods & Data
Input
  • Expresson data file = KIRC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

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

  • Number of patients = 533

  • Number of genes = 18278

  • Number of clinical features = 12

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)