Correlation between mRNAseq expression and clinical features
Kidney Renal Papillary 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/C1G44PQ0
Overview
Introduction

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

Summary

Testing the association between 17999 genes and 12 clinical features across 290 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'.

    • IGF2BP3|10643 ,  NUSAP1|51203 ,  CDCA2|157313 ,  OIP5|11339 ,  RAET1K|646024 ,  ...

  • 30 genes correlated to 'YEARS_TO_BIRTH'.

    • LDHD|197257 ,  HIBCH|26275 ,  MFSD3|113655 ,  SLC22A18|5002 ,  TNFAIP1|7126 ,  ...

  • 30 genes correlated to 'PATHOLOGIC_STAGE'.

    • KIF20A|10112 ,  EPR1|8475 ,  TPX2|22974 ,  CEP55|55165 ,  CENPF|1063 ,  ...

  • 30 genes correlated to 'PATHOLOGY_T_STAGE'.

    • EPR1|8475 ,  BUB1|699 ,  TPX2|22974 ,  CEP55|55165 ,  NUF2|83540 ,  ...

  • 30 genes correlated to 'PATHOLOGY_N_STAGE'.

    • USP13|8975 ,  NEK2|4751 ,  L1CAM|3897 ,  ACAD8|27034 ,  TCTA|6988 ,  ...

  • 30 genes correlated to 'PATHOLOGY_M_STAGE'.

    • LYAR|55646 ,  MKI67IP|84365 ,  PABPC4|8761 ,  RPL6|6128 ,  LOC728643|728643 ,  ...

  • 8 genes correlated to 'GENDER'.

    • HDHD1A|8226 ,  NCRNA00183|554203 ,  SLC2A9|56606 ,  NLRP6|171389 ,  AOX1|316 ,  ...

  • 30 genes correlated to 'KARNOFSKY_PERFORMANCE_SCORE'.

    • STK19|8859 ,  LOC284440|284440 ,  PNPLA7|375775 ,  C9ORF95|54981 ,  GTF2H4|2968 ,  ...

  • 30 genes correlated to 'RACE'.

    • NOTCH2NL|388677 ,  LRRC37A2|474170 ,  GSTM3|2947 ,  CRYBB2|1415 ,  LOC90784|90784 ,  ...

  • 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=17 younger N=13
PATHOLOGIC_STAGE Kruskal-Wallis test N=30        
PATHOLOGY_T_STAGE Spearman correlation test N=30 higher stage N=30 lower stage N=0
PATHOLOGY_N_STAGE Spearman correlation test N=30 higher stage N=23 lower stage N=7
PATHOLOGY_M_STAGE Wilcoxon test N=30 class1 N=30 class0 N=0
GENDER Wilcoxon test N=8 male N=8 female N=0
KARNOFSKY_PERFORMANCE_SCORE Spearman correlation test N=30 higher score N=24 lower score N=6
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) 0.1-194.8 (median=25.3)
  censored N = 245
  death N = 44
     
  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
IGF2BP3|10643 6.99e-15 1.3e-10 0.82
NUSAP1|51203 1.25e-11 9.2e-08 0.781
CDCA2|157313 1.54e-11 9.2e-08 0.782
OIP5|11339 2.26e-11 1e-07 0.789
RAET1K|646024 3.66e-11 1.3e-07 0.774
TPX2|22974 7.99e-11 2.2e-07 0.812
KIF4A|24137 9.79e-11 2.2e-07 0.788
ASPM|259266 1.01e-10 2.2e-07 0.806
C20ORF132|140699 1.12e-10 2.2e-07 0.245
PRC1|9055 1.41e-10 2.5e-07 0.789
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) 61.45 (12)
  Significant markers N = 30
  pos. correlated 17
  neg. correlated 13
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
LDHD|197257 0.2957 3.705e-07 0.00667
HIBCH|26275 0.2879 7.666e-07 0.0069
MFSD3|113655 0.2787 1.758e-06 0.00909
SLC22A18|5002 0.2721 3.124e-06 0.00909
TNFAIP1|7126 -0.2705 3.611e-06 0.00909
BCAT2|587 0.2667 4.971e-06 0.00909
ATPAF1|64756 0.2662 5.177e-06 0.00909
SLC22A18AS|5003 0.2659 5.319e-06 0.00909
STAT3|6774 -0.2658 5.374e-06 0.00909
KLHL29|114818 -0.2655 5.501e-06 0.00909
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 172
  STAGE II 21
  STAGE III 52
  STAGE IV 15
     
  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 3.635e-16 6.54e-12
EPR1|8475 7.649e-16 6.88e-12
TPX2|22974 2.208e-15 9.31e-12
CEP55|55165 2.319e-15 9.31e-12
CENPF|1063 3.767e-15 9.31e-12
KIFC1|3833 3.864e-15 9.31e-12
CDCA2|157313 4.107e-15 9.31e-12
NUF2|83540 4.138e-15 9.31e-12
NEK2|4751 5.837e-15 1.16e-11
CENPA|1058 6.464e-15 1.16e-11
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) 1.55 (0.84)
  N
  T1 193
  T2 33
  T3 60
  T4 2
     
  Significant markers N = 30
  pos. correlated 30
  neg. correlated 0
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
EPR1|8475 0.4904 2.385e-18 4.29e-14
BUB1|699 0.477 9.105e-18 8.19e-14
TPX2|22974 0.464 8.738e-17 4e-13
CEP55|55165 0.4639 8.9e-17 4e-13
NUF2|83540 0.4599 1.763e-16 5.33e-13
CDCA2|157313 0.4599 1.978e-16 5.33e-13
EXO1|9156 0.459 2.072e-16 5.33e-13
CDCA8|55143 0.4579 2.466e-16 5.55e-13
UCK2|7371 0.4544 4.41e-16 8.48e-13
NEK2|4751 0.4555 4.714e-16 8.48e-13
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) 0.41 (0.59)
  N
  N0 50
  N1 24
  N2 4
     
  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
USP13|8975 0.5993 6.733e-09 6.19e-05
NEK2|4751 0.5933 1.042e-08 6.19e-05
L1CAM|3897 0.5907 1.252e-08 6.19e-05
ACAD8|27034 -0.5893 1.377e-08 6.19e-05
TCTA|6988 -0.5842 1.965e-08 6.56e-05
TBX18|9096 0.5988 2.188e-08 6.56e-05
THBS4|7060 0.5778 3.036e-08 6.87e-05
C9ORF140|89958 0.5778 3.055e-08 6.87e-05
TPX2|22974 0.576 3.442e-08 6.88e-05
NAP1L1|4673 0.5712 4.732e-08 8.22e-05
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 95
  class1 9
     
  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
LYAR|55646 817 6.879e-06 0.0615 0.9556
MKI67IP|84365 807 1.177e-05 0.0615 0.9439
PABPC4|8761 798 1.888e-05 0.0615 0.9333
RPL6|6128 797 1.988e-05 0.0615 0.9322
LOC728643|728643 791 2.707e-05 0.0615 0.9251
ZBTB2|57621 790 2.849e-05 0.0615 0.924
RPL10A|4736 787 3.317e-05 0.0615 0.9205
NAP1L1|4673 786 3.488e-05 0.0615 0.9193
BYSL|705 785 3.668e-05 0.0615 0.9181
NOLC1|9221 784 3.857e-05 0.0615 0.917
Clinical variable #7: 'GENDER'

8 genes related to 'GENDER'.

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

GENDER Labels N
  FEMALE 76
  MALE 214
     
  Significant markers N = 8
  Higher in MALE 8
  Higher in FEMALE 0
List of 8 genes differentially expressed by 'GENDER'

Table S14.  Get Full Table List of 8 genes differentially expressed by 'GENDER'. 22 significant gene(s) located in sex chromosomes is(are) filtered out.

W(pos if higher in 'MALE') wilcoxontestP Q AUC
HDHD1A|8226 2882 6.331e-17 1.14e-13 0.8228
NCRNA00183|554203 2931 1.223e-16 2e-13 0.8198
SLC2A9|56606 13056 4.513e-15 5.42e-12 0.8028
NLRP6|171389 12508 3.998e-14 4.23e-11 0.7942
AOX1|316 12711 3.089e-13 2.5e-10 0.7815
MSH6|2956 3665 1.143e-12 7.91e-10 0.7747
C1ORF186|440712 12574 1.524e-12 9.46e-10 0.7731
ZMYND12|84217 12476 4.638e-12 2.78e-09 0.7671
Clinical variable #8: 'KARNOFSKY_PERFORMANCE_SCORE'

30 genes related to 'KARNOFSKY_PERFORMANCE_SCORE'.

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

KARNOFSKY_PERFORMANCE_SCORE Mean (SD) 87.66 (22)
  Significant markers N = 30
  pos. correlated 24
  neg. correlated 6
List of top 10 genes differentially expressed by 'KARNOFSKY_PERFORMANCE_SCORE'

Table S16.  Get Full Table List of top 10 genes significantly correlated to 'KARNOFSKY_PERFORMANCE_SCORE' by Spearman correlation test

SpearmanCorr corrP Q
STK19|8859 0.4914 5.671e-06 0.0207
LOC284440|284440 0.49 6.087e-06 0.0207
PNPLA7|375775 0.4868 7.139e-06 0.0207
C9ORF95|54981 0.4862 7.379e-06 0.0207
GTF2H4|2968 0.485 7.8e-06 0.0207
TUBE1|51175 0.4773 1.141e-05 0.0207
C14ORF181|400223 0.4762 1.199e-05 0.0207
DUT|1854 0.4723 1.449e-05 0.0207
PRR11|55771 -0.4889 1.52e-05 0.0207
PTGR2|145482 0.47 1.611e-05 0.0207
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) 32.08 (27)
  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) 1972.29 (16)
  Significant markers N = 0
Clinical variable #11: 'RACE'

30 genes related to 'RACE'.

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

RACE Labels N
  AMERICAN INDIAN OR ALASKA NATIVE 2
  ASIAN 6
  BLACK OR AFRICAN AMERICAN 61
  WHITE 206
     
  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
NOTCH2NL|388677 1.483e-12 2.67e-08
LRRC37A2|474170 6.278e-10 5.65e-06
GSTM3|2947 2.243e-08 0.000135
CRYBB2|1415 1.599e-07 0.000719
LOC90784|90784 2.342e-07 0.000843
BEGAIN|57596 7.97e-07 0.00239
CN5H6.4|150384 1.255e-06 0.00323
LOC441455|441455 2.839e-06 0.00608
ULK4|54986 3.202e-06 0.00608
LQK1|642946 3.378e-06 0.00608
Clinical variable #12: 'ETHNICITY'

No gene related to 'ETHNICITY'.

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

ETHNICITY Labels N
  HISPANIC OR LATINO 12
  NOT HISPANIC OR LATINO 242
     
  Significant markers N = 0
Methods & Data
Input
  • Expresson data file = KIRP-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

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

  • Number of patients = 290

  • Number of genes = 17999

  • 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)