Correlation between mRNAseq expression and clinical features
Pan-kidney cohort (KICH+KIRC+KIRP) (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1736Q98
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/C1736Q98
Overview
Introduction

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

Summary

Testing the association between 18216 genes and 14 clinical features across 889 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'.

    • ACAT1|38 ,  ACSS3|79611 ,  ANLN|54443 ,  ASPM|259266 ,  AUH|549 ,  ...

  • 30 genes correlated to 'YEARS_TO_BIRTH'.

    • KIT|3815 ,  CYTSB|92521 ,  NRXN3|9369 ,  MEX3C|51320 ,  ZC3H4|23211 ,  ...

  • 30 genes correlated to 'PATHOLOGIC_STAGE'.

    • KIF20A|10112 ,  NCAPG|64151 ,  CEP55|55165 ,  UBE2C|11065 ,  SKA1|220134 ,  ...

  • 30 genes correlated to 'PATHOLOGY_T_STAGE'.

    • UBE2C|11065 ,  BUB1|699 ,  NCAPG|64151 ,  CCNB2|9133 ,  TPX2|22974 ,  ...

  • 30 genes correlated to 'PATHOLOGY_N_STAGE'.

    • UBE2T|29089 ,  PKMYT1|9088 ,  C16ORF59|80178 ,  BIRC5|332 ,  NEK2|4751 ,  ...

  • 30 genes correlated to 'PATHOLOGY_M_STAGE'.

    • NCAPG|64151 ,  CEP55|55165 ,  BIRC5|332 ,  OIP5|11339 ,  PTTG1|9232 ,  ...

  • 7 genes correlated to 'GENDER'.

    • NCRNA00183|554203 ,  HDHD1A|8226 ,  DNAJB13|374407 ,  CYORF15A|246126 ,  CCDC146|57639 ,  ...

  • 30 genes correlated to 'KARNOFSKY_PERFORMANCE_SCORE'.

    • PTGR2|145482 ,  CYP1B1|1545 ,  PHF7|51533 ,  GKAP1|80318 ,  PATZ1|23598 ,  ...

  • 30 genes correlated to 'HISTOLOGICAL_TYPE'.

    • NDUFA4L2|56901 ,  ELTD1|64123 ,  GPR4|2828 ,  FLT1|2321 ,  CDH13|1012 ,  ...

  • 21 genes correlated to 'YEAR_OF_TOBACCO_SMOKING_ONSET'.

    • AGK|55750 ,  POM121|9883 ,  CD1B|910 ,  PPAPDC1B|84513 ,  NOM1|64434 ,  ...

  • 30 genes correlated to 'RACE'.

    • NOTCH2NL|388677 ,  TUBB8|347688 ,  LOC90784|90784 ,  ULK4|54986 ,  CROCCL1|84809 ,  ...

  • No genes correlated to 'RADIATION_THERAPY', 'NUMBER_PACK_YEARS_SMOKED', 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=7 younger N=23
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=29 lower stage N=1
PATHOLOGY_M_STAGE Wilcoxon test N=30 class1 N=30 class0 N=0
GENDER Wilcoxon test N=7 male N=7 female N=0
RADIATION_THERAPY Wilcoxon test   N=0        
KARNOFSKY_PERFORMANCE_SCORE Spearman correlation test N=30 higher score N=17 lower score N=13
HISTOLOGICAL_TYPE Kruskal-Wallis test N=30        
NUMBER_PACK_YEARS_SMOKED Spearman correlation test   N=0        
YEAR_OF_TOBACCO_SMOKING_ONSET Spearman correlation test N=21 higher year_of_tobacco_smoking_onset N=6 lower year_of_tobacco_smoking_onset N=15
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) 0.1-194.8 (median=35.9)
  censored N = 659
  death N = 229
     
  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
ACAT1|38 0 0 0.323
ACSS3|79611 0 0 0.335
ANLN|54443 0 0 0.684
ASPM|259266 0 0 0.706
AUH|549 0 0 0.325
AURKB|9212 0 0 0.703
BIRC5|332 0 0 0.718
BLM|641 0 0 0.67
BUB1B|701 0 0 0.68
BUB1|699 0 0 0.681
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) 60.2 (13)
  Significant markers N = 30
  pos. correlated 7
  neg. correlated 23
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
KIT|3815 -0.224 1.668e-11 3.04e-07
CYTSB|92521 -0.2156 9.615e-11 7.57e-07
NRXN3|9369 -0.2144 1.247e-10 7.57e-07
MEX3C|51320 -0.2094 3.307e-10 1.51e-06
ZC3H4|23211 -0.206 6.437e-10 1.79e-06
VKORC1|79001 0.2059 6.53e-10 1.79e-06
NKAPL|222698 -0.2064 6.873e-10 1.79e-06
ZMIZ1|57178 -0.2047 8.272e-10 1.88e-06
BACH2|60468 -0.2023 1.307e-09 2.5e-06
DACT1|51339 -0.2021 1.37e-09 2.5e-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 460
  STAGE II 103
  STAGE III 189
  STAGE IV 105
     
  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
KIF20A|10112 2.261e-34 4.12e-30
NCAPG|64151 9.654e-33 7.47e-29
CEP55|55165 1.56e-32 7.47e-29
UBE2C|11065 1.717e-32 7.47e-29
SKA1|220134 2.051e-32 7.47e-29
TPX2|22974 9.008e-32 2.73e-28
BIRC5|332 1.666e-31 4.34e-28
HJURP|55355 5.509e-31 1.25e-27
PTTG1|9232 8.192e-31 1.66e-27
CENPF|1063 1.164e-30 1.95e-27
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) 1.78 (0.93)
  N
  T1 487
  T2 127
  T3 258
  T4 15
     
  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
UBE2C|11065 0.3883 2.632e-33 4.8e-29
BUB1|699 0.3857 8.245e-33 7.51e-29
NCAPG|64151 0.3798 8.626e-32 5.24e-28
CCNB2|9133 0.3772 2.218e-31 1.01e-27
TPX2|22974 0.3727 1.278e-30 4.65e-27
GTSE1|51512 0.3712 2.533e-30 7.42e-27
KIF20A|10112 0.371 2.85e-30 7.42e-27
SKA1|220134 0.3699 3.757e-30 8.55e-27
CENPF|1063 0.3646 2.821e-29 5.71e-26
CEP55|55165 0.3641 3.367e-29 6.13e-26
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) 0.15 (0.4)
  N
  N0 330
  N1 43
  N2 6
     
  Significant markers N = 30
  pos. correlated 29
  neg. correlated 1
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
UBE2T|29089 0.4306 1.547e-18 2.82e-14
PKMYT1|9088 0.4183 1.923e-17 1.75e-13
C16ORF59|80178 0.3972 9.828e-16 5.97e-12
BIRC5|332 0.3875 4.99e-15 2.27e-11
NEK2|4751 0.3828 1.125e-14 4.1e-11
AURKB|9212 0.3817 1.356e-14 4.12e-11
FASN|2194 0.3807 1.616e-14 4.21e-11
CDC20|991 0.3755 3.907e-14 8.82e-11
PLK1|5347 0.3748 4.36e-14 8.82e-11
PYCR1|5831 0.3735 5.406e-14 9.69e-11
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 551
  class1 90
     
  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
NCAPG|64151 37382 7.968e-15 7.43e-11 0.7552
CEP55|55165 37388 1.067e-14 7.43e-11 0.7539
BIRC5|332 37226 1.691e-14 7.43e-11 0.752
OIP5|11339 37081 2.468e-14 7.43e-11 0.7505
PTTG1|9232 37172 2.997e-14 7.43e-11 0.7496
SKA1|220134 37165 3.099e-14 7.43e-11 0.7494
CENPA|1058 37095 3.16e-14 7.43e-11 0.7494
IGF2BP3|10643 37154 3.264e-14 7.43e-11 0.7492
CCNB2|9133 36972 7.683e-14 1.4e-10 0.7456
TMEM25|84866 12623 7.864e-14 1.4e-10 0.7455
Clinical variable #7: 'GENDER'

7 genes related to 'GENDER'.

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

GENDER Labels N
  FEMALE 291
  MALE 598
     
  Significant markers N = 7
  Higher in MALE 7
  Higher in FEMALE 0
List of 7 genes differentially expressed by 'GENDER'

Table S14.  Get Full Table List of 7 genes differentially expressed by 'GENDER'. 23 significant gene(s) located in sex chromosomes is(are) filtered out.

W(pos if higher in 'MALE') wilcoxontestP Q AUC
NCRNA00183|554203 29002 1.204e-58 2.19e-55 0.8333
HDHD1A|8226 37923.5 1.688e-42 2.05e-39 0.7821
DNAJB13|374407 119293.5 9.91e-36 9.03e-33 0.7656
CYORF15A|246126 34157 6.876e-30 5.01e-27 0.9411
CCDC146|57639 126842 1.442e-28 1.01e-25 0.7289
PROM1|8842 122950.5 2.57e-28 1.73e-25 0.7302
RERG|85004 126178 1.118e-27 7.28e-25 0.7251
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 415
  YES 3
     
  Significant markers N = 0
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) 88.39 (22)
  Significant markers N = 30
  pos. correlated 17
  neg. correlated 13
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
PTGR2|145482 0.3776 3.327e-06 0.0606
CYP1B1|1545 -0.3506 1.761e-05 0.128
PHF7|51533 0.3344 4.47e-05 0.128
GKAP1|80318 0.3328 4.882e-05 0.128
PATZ1|23598 0.3311 5.361e-05 0.128
RHBDL2|54933 -0.3311 5.378e-05 0.128
CIRBP|1153 0.3284 6.219e-05 0.128
SAPS2|9701 0.3274 6.579e-05 0.128
FNTB|2342 0.3264 6.947e-05 0.128
DHCR24|1718 -0.3261 7.037e-05 0.128
Clinical variable #10: 'HISTOLOGICAL_TYPE'

30 genes related to 'HISTOLOGICAL_TYPE'.

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

HISTOLOGICAL_TYPE Labels N
  KIDNEY CHROMOPHOBE 66
  KIDNEY CLEAR CELL RENAL CARCINOMA 533
  KIDNEY PAPILLARY RENAL CELL CARCINOMA 290
     
  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
NDUFA4L2|56901 4.007e-129 7.3e-125
ELTD1|64123 2.568e-128 2.34e-124
GPR4|2828 5.462e-128 3.1e-124
FLT1|2321 6.811e-128 3.1e-124
CDH13|1012 2.064e-127 7.52e-124
MYCT1|80177 6.607e-127 2.01e-123
VEGFA|7422 9.793e-127 2.3e-123
C3ORF70|285382 1.009e-126 2.3e-123
APLN|8862 2.005e-126 4.06e-123
ERG|2078 1.787e-125 3.26e-122
Clinical variable #11: 'NUMBER_PACK_YEARS_SMOKED'

No gene related to 'NUMBER_PACK_YEARS_SMOKED'.

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

NUMBER_PACK_YEARS_SMOKED Mean (SD) 30.63 (25)
  Significant markers N = 0
Clinical variable #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

21 genes related to 'YEAR_OF_TOBACCO_SMOKING_ONSET'.

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

YEAR_OF_TOBACCO_SMOKING_ONSET Mean (SD) 1973.56 (16)
  Significant markers N = 21
  pos. correlated 6
  neg. correlated 15
List of top 10 genes differentially expressed by 'YEAR_OF_TOBACCO_SMOKING_ONSET'

Table S22.  Get Full Table List of top 10 genes significantly correlated to 'YEAR_OF_TOBACCO_SMOKING_ONSET' by Spearman correlation test

SpearmanCorr corrP Q
AGK|55750 -0.4665 2.461e-05 0.275
POM121|9883 -0.4599 3.303e-05 0.275
CD1B|910 0.5901 6.129e-05 0.275
PPAPDC1B|84513 0.4408 7.544e-05 0.275
NOM1|64434 -0.4385 8.322e-05 0.275
SLC2A13|114134 -0.4325 0.0001066 0.275
PTCD1|26024 -0.4264 0.0001363 0.275
IFITM1|8519 0.4264 0.0001367 0.275
NAPEPLD|222236 -0.4253 0.0001428 0.275
TYW1|55253 -0.4226 0.0001587 0.275
Clinical variable #13: 'RACE'

30 genes related to 'RACE'.

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

RACE Labels N
  AMERICAN INDIAN OR ALASKA NATIVE 2
  ASIAN 16
  BLACK OR AFRICAN AMERICAN 121
  WHITE 726
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'RACE'

Table S24.  Get Full Table List of top 10 genes differentially expressed by 'RACE'

kruskal_wallis_P Q
NOTCH2NL|388677 1.537e-25 2.8e-21
TUBB8|347688 2.797e-18 2.55e-14
LOC90784|90784 2.497e-16 1.52e-12
ULK4|54986 3.656e-15 1.66e-11
CROCCL1|84809 3.855e-14 1.4e-10
LOC653113|653113 5.353e-14 1.63e-10
LRRC37A2|474170 8.623e-14 2.24e-10
PRSS45|377047 6.031e-13 1.31e-09
CRYBB2|1415 6.49e-13 1.31e-09
FAM22A|728118 8.785e-13 1.6e-09
Clinical variable #14: 'ETHNICITY'

No gene related to 'ETHNICITY'.

Table S25.  Basic characteristics of clinical feature: 'ETHNICITY'

ETHNICITY Labels N
  HISPANIC OR LATINO 42
  NOT HISPANIC OR LATINO 629
     
  Significant markers N = 0
Methods & Data
Input

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

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

  • Number of patients = 889

  • Number of genes = 18216

  • Number of clinical features = 14

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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