Correlation between mRNAseq expression and clinical features
Head and Neck Squamous Cell Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1JS9PTD
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/C1JS9PTD
Overview
Introduction

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

Summary

Testing the association between 18378 genes and 14 clinical features across 520 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 12 clinical features related to at least one genes.

  • 30 genes correlated to 'DAYS_TO_DEATH_OR_LAST_FUP'.

    • AIG1|51390 ,  SLC35E2|9906 ,  FGD3|89846 ,  DKK1|22943 ,  NLGN4Y|22829 ,  ...

  • 30 genes correlated to 'YEARS_TO_BIRTH'.

    • C1ORF103|55791 ,  RNASE3|6037 ,  PER3|8863 ,  MUTED|63915 ,  ABAT|18 ,  ...

  • 30 genes correlated to 'PATHOLOGIC_STAGE'.

    • ZC3HAV1|56829 ,  TRIM25|7706 ,  WDR37|22884 ,  MYD88|4615 ,  ITPR2|3709 ,  ...

  • 30 genes correlated to 'PATHOLOGY_T_STAGE'.

    • C5ORF20|140947 ,  TCEANC|170082 ,  RNPC3|55599 ,  FUT7|2529 ,  ADM|133 ,  ...

  • 30 genes correlated to 'PATHOLOGY_N_STAGE'.

    • MPZL2|10205 ,  ARHGAP32|9743 ,  SPRR2F|6705 ,  TRIM29|23650 ,  IL1F5|26525 ,  ...

  • 6 genes correlated to 'GENDER'.

    • HDHD1A|8226 ,  CYORF15A|246126 ,  CYORF15B|84663 ,  CA5BP|340591 ,  FAM64A|54478 ,  ...

  • 30 genes correlated to 'RADIATION_THERAPY'.

    • MYOM3|127294 ,  CRTC2|200186 ,  LOC284900|284900 ,  ILF2|3608 ,  MYH13|8735 ,  ...

  • 30 genes correlated to 'HISTOLOGICAL_TYPE'.

    • EHD2|30846 ,  NCRNA00201|284702 ,  ACTB|60 ,  NFYB|4801 ,  SUGT1L1|283507 ,  ...

  • 30 genes correlated to 'NUMBER_PACK_YEARS_SMOKED'.

    • ALDOC|230 ,  SLC5A5|6528 ,  CAND1|55832 ,  PANX2|56666 ,  UBE2O|63893 ,  ...

  • 30 genes correlated to 'YEAR_OF_TOBACCO_SMOKING_ONSET'.

    • SMAD6|4091 ,  ARSE|415 ,  AREG|374 ,  FMO3|2328 ,  TNFSF4|7292 ,  ...

  • 30 genes correlated to 'NUMBER_OF_LYMPH_NODES'.

    • NLRX1|79671 ,  MPZL2|10205 ,  MASP1|5648 ,  ARL4C|10123 ,  SLC5A10|125206 ,  ...

  • 30 genes correlated to 'RACE'.

    • LOC90784|90784 ,  SERHL2|253190 ,  LRRC37A2|474170 ,  ULK4|54986 ,  GSTM1|2944 ,  ...

  • No genes correlated to 'PATHOLOGY_M_STAGE', 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=15 younger N=15
PATHOLOGIC_STAGE Kruskal-Wallis test N=30        
PATHOLOGY_T_STAGE Spearman correlation test N=30 higher stage N=6 lower stage N=24
PATHOLOGY_N_STAGE Spearman correlation test N=30 higher stage N=3 lower stage N=27
PATHOLOGY_M_STAGE Wilcoxon test   N=0        
GENDER Wilcoxon test N=6 male N=6 female N=0
RADIATION_THERAPY Wilcoxon test N=30 yes N=30 no N=0
HISTOLOGICAL_TYPE Kruskal-Wallis test N=30        
NUMBER_PACK_YEARS_SMOKED Spearman correlation test N=30 higher number_pack_years_smoked N=26 lower number_pack_years_smoked N=4
YEAR_OF_TOBACCO_SMOKING_ONSET Spearman correlation test N=30 higher year_of_tobacco_smoking_onset N=5 lower year_of_tobacco_smoking_onset N=25
NUMBER_OF_LYMPH_NODES Spearman correlation test N=30 higher number_of_lymph_nodes N=6 lower number_of_lymph_nodes N=24
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) 0.1-211 (median=21.5)
  censored N = 299
  death N = 220
     
  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
AIG1|51390 2.14e-06 0.02 0.601
SLC35E2|9906 4.11e-06 0.02 0.407
FGD3|89846 4.7e-06 0.02 0.383
DKK1|22943 5.33e-06 0.02 0.593
NLGN4Y|22829 6.37e-06 0.02 0.414
CD79A|973 8.51e-06 0.02 0.393
TCERG1|10915 9.3e-06 0.02 0.484
FRMD5|84978 1.04e-05 0.02 0.614
UTY|7404 1.08e-05 0.02 0.404
KIAA0467|23334 1.11e-05 0.02 0.406
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) 60.87 (12)
  Significant markers N = 30
  pos. correlated 15
  neg. correlated 15
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
C1ORF103|55791 -0.2149 7.758e-07 0.00811
RNASE3|6037 0.2655 8.83e-07 0.00811
PER3|8863 -0.2089 1.577e-06 0.00945
MUTED|63915 -0.2066 2.057e-06 0.00945
ABAT|18 -0.1974 5.899e-06 0.0217
GABRR1|2569 0.2002 1.361e-05 0.0317
KCNS1|3787 -0.1954 1.561e-05 0.0317
C19ORF76|199800 0.1881 1.601e-05 0.0317
GPSM2|29899 -0.1881 1.606e-05 0.0317
CNTN5|53942 0.2205 1.726e-05 0.0317
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 27
  STAGE II 74
  STAGE III 81
  STAGE IVA 253
  STAGE IVB 12
  STAGE IVC 1
     
  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
ZC3HAV1|56829 2.635e-08 0.000416
TRIM25|7706 4.526e-08 0.000416
WDR37|22884 5.312e-06 0.0325
MYD88|4615 1.202e-05 0.0552
ITPR2|3709 2.305e-05 0.06
DDIT4|54541 2.608e-05 0.06
NCOA5|57727 2.962e-05 0.06
LOC93622|93622 3.119e-05 0.06
MTHFR|4524 3.196e-05 0.06
C12ORF47|51275 4.059e-05 0.06
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) 2.87 (1)
  N
  T0 1
  T1 48
  T2 136
  T3 99
  T4 174
     
  Significant markers N = 30
  pos. correlated 6
  neg. correlated 24
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
C5ORF20|140947 -0.3031 4.865e-11 8.94e-07
TCEANC|170082 -0.2863 4.333e-10 3.98e-06
RNPC3|55599 -0.2808 9.538e-10 5.84e-06
FUT7|2529 -0.2761 1.929e-09 8.37e-06
ADM|133 0.2746 2.278e-09 8.37e-06
P2RY13|53829 -0.2687 5.33e-09 1.3e-05
TLR10|81793 -0.2697 5.457e-09 1.3e-05
LRRC8A|56262 0.268 5.669e-09 1.3e-05
MSL3|10943 -0.2651 8.315e-09 1.7e-05
SPIB|6689 -0.2637 1.172e-08 2.13e-05
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) 1.02 (0.95)
  N
  N0 176
  N1 67
  N2 169
  N3 8
     
  Significant markers N = 30
  pos. correlated 3
  neg. correlated 27
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
MPZL2|10205 -0.2949 7.168e-10 1.32e-05
ARHGAP32|9743 -0.2797 5.452e-09 4.26e-05
SPRR2F|6705 -0.2801 6.981e-09 4.26e-05
TRIM29|23650 -0.2756 9.276e-09 4.26e-05
IL1F5|26525 -0.2683 2.446e-08 8.99e-05
TGM1|7051 -0.2628 4.584e-08 0.000114
APOC1|341 0.2622 4.946e-08 0.000114
PDXP|57026 0.2617 5.233e-08 0.000114
SPRR2D|6703 -0.2608 5.847e-08 0.000114
WDR37|22884 -0.2603 6.228e-08 0.000114
Clinical variable #6: 'PATHOLOGY_M_STAGE'

No gene related to 'PATHOLOGY_M_STAGE'.

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

PATHOLOGY_M_STAGE Labels N
  class0 186
  class1 1
     
  Significant markers N = 0
Clinical variable #7: 'GENDER'

6 genes related to 'GENDER'.

Table S12.  Basic characteristics of clinical feature: 'GENDER'

GENDER Labels N
  FEMALE 136
  MALE 384
     
  Significant markers N = 6
  Higher in MALE 6
  Higher in FEMALE 0
List of 6 genes differentially expressed by 'GENDER'

Table S13.  Get Full Table List of 6 genes differentially expressed by 'GENDER'. 24 significant gene(s) located in sex chromosomes is(are) filtered out.

W(pos if higher in 'MALE') wilcoxontestP Q AUC
HDHD1A|8226 10212 4.619e-26 7.07e-23 0.8045
CYORF15A|246126 10330 4.371e-18 4.02e-15 0.9989
CYORF15B|84663 9466 1.291e-16 1.08e-13 0.9938
CA5BP|340591 15274 6.144e-13 4.71e-10 0.7075
FAM64A|54478 36506 5.114e-12 3.48e-09 0.699
ZNF232|7775 35500.5 4.529e-10 2.87e-07 0.6798
Clinical variable #8: 'RADIATION_THERAPY'

30 genes related to 'RADIATION_THERAPY'.

Table S14.  Basic characteristics of clinical feature: 'RADIATION_THERAPY'

RADIATION_THERAPY Labels N
  NO 161
  YES 297
     
  Significant markers N = 30
  Higher in YES 30
  Higher in NO 0
List of top 10 genes differentially expressed by 'RADIATION_THERAPY'

Table S15.  Get Full Table List of top 10 genes differentially expressed by 'RADIATION_THERAPY'

W(pos if higher in 'YES') wilcoxontestP Q AUC
MYOM3|127294 16857 1.851e-07 0.00265 0.6475
CRTC2|200186 30848 2.884e-07 0.00265 0.6451
LOC284900|284900 30535 9.612e-07 0.00589 0.6386
ILF2|3608 30368 1.789e-06 0.00731 0.6351
MYH13|8735 9578 2.166e-06 0.00731 0.6533
ALKBH8|91801 17528 2.387e-06 0.00731 0.6334
SYNPO2L|79933 17230 3.078e-06 0.00734 0.6327
LOC285074|285074 30186 3.461e-06 0.00734 0.6313
AASDHPPT|60496 17701 4.441e-06 0.00734 0.6298
PHF10|55274 30077 5.097e-06 0.00734 0.629
Clinical variable #9: 'HISTOLOGICAL_TYPE'

30 genes related to 'HISTOLOGICAL_TYPE'.

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

HISTOLOGICAL_TYPE Labels N
  HEAD & NECK SQUAMOUS CELL CARCINOMA 509
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE 10
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT 1
     
  Significant markers N = 30
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'

kruskal_wallis_P Q
EHD2|30846 1.893e-06 0.0163
NCRNA00201|284702 3.919e-06 0.0163
ACTB|60 4.491e-06 0.0163
NFYB|4801 4.589e-06 0.0163
SUGT1L1|283507 6.96e-06 0.0163
RALGPS1|9649 9.695e-06 0.0163
KIAA0907|22889 1.087e-05 0.0163
RCOR3|55758 1.109e-05 0.0163
C1ORF77|26097 1.286e-05 0.0163
PLOD1|5351 1.319e-05 0.0163
Clinical variable #10: 'NUMBER_PACK_YEARS_SMOKED'

30 genes related to 'NUMBER_PACK_YEARS_SMOKED'.

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

NUMBER_PACK_YEARS_SMOKED Mean (SD) 45.83 (35)
  Significant markers N = 30
  pos. correlated 26
  neg. correlated 4
List of top 10 genes differentially expressed by 'NUMBER_PACK_YEARS_SMOKED'

Table S19.  Get Full Table List of top 10 genes significantly correlated to 'NUMBER_PACK_YEARS_SMOKED' by Spearman correlation test

SpearmanCorr corrP Q
ALDOC|230 0.2901 3.779e-07 0.00694
SLC5A5|6528 0.2923 1.064e-06 0.00764
CAND1|55832 0.271 2.224e-06 0.00764
PANX2|56666 0.2694 2.561e-06 0.00764
UBE2O|63893 0.2681 2.877e-06 0.00764
DPH3|285381 -0.265 3.769e-06 0.00764
TMSL3|7117 -0.2648 3.861e-06 0.00764
TMTC3|160418 0.2642 4.046e-06 0.00764
ABCC1|4363 0.264 4.145e-06 0.00764
C12ORF66|144577 0.2629 4.558e-06 0.00764
Clinical variable #11: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

30 genes related to 'YEAR_OF_TOBACCO_SMOKING_ONSET'.

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

YEAR_OF_TOBACCO_SMOKING_ONSET Mean (SD) 1967.37 (13)
  Significant markers N = 30
  pos. correlated 5
  neg. correlated 25
List of top 10 genes differentially expressed by 'YEAR_OF_TOBACCO_SMOKING_ONSET'

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

SpearmanCorr corrP Q
SMAD6|4091 -0.2736 3.24e-06 0.0347
ARSE|415 -0.2732 3.775e-06 0.0347
AREG|374 0.2624 8.293e-06 0.0406
FMO3|2328 -0.2579 1.197e-05 0.0406
TNFSF4|7292 -0.257 1.29e-05 0.0406
ST8SIA4|7903 -0.2566 1.324e-05 0.0406
SIPA1L3|23094 -0.2489 2.433e-05 0.0537
DISC1|27185 -0.2466 2.905e-05 0.0537
TCN2|6948 -0.2466 2.921e-05 0.0537
MSR1|4481 -0.2466 2.923e-05 0.0537
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) 2.2 (4.3)
  Significant markers N = 30
  pos. correlated 6
  neg. correlated 24
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
NLRX1|79671 -0.2824 7.304e-09 0.000134
MPZL2|10205 -0.2721 2.64e-08 0.000166
MASP1|5648 -0.2722 2.707e-08 0.000166
ARL4C|10123 0.2665 5.168e-08 0.000237
SLC5A10|125206 -0.2574 1.546e-07 0.000461
TRIM29|23650 -0.2566 1.649e-07 0.000461
IL1F5|26525 -0.2563 1.755e-07 0.000461
ARHGAP32|9743 -0.2541 2.18e-07 0.000501
PPEF1|5475 0.2537 2.521e-07 0.000515
RNF222|643904 -0.2506 3.963e-07 0.000598
Clinical variable #13: 'RACE'

30 genes related to 'RACE'.

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

RACE Labels N
  AMERICAN INDIAN OR ALASKA NATIVE 2
  ASIAN 11
  BLACK OR AFRICAN AMERICAN 48
  WHITE 444
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'RACE'

Table S25.  Get Full Table List of top 10 genes differentially expressed by 'RACE'

kruskal_wallis_P Q
LOC90784|90784 1.568e-08 0.000288
SERHL2|253190 5.063e-08 0.000426
LRRC37A2|474170 6.954e-08 0.000426
ULK4|54986 2.663e-07 0.00122
GSTM1|2944 4.364e-07 0.0016
TBL2|26608 7.838e-07 0.0024
CRYBB2|1415 1.033e-06 0.00271
MXRA7|439921 1.573e-06 0.00361
SERHL|94009 2.629e-06 0.00533
POLR2J2|246721 3.521e-06 0.00533
Clinical variable #14: 'ETHNICITY'

No gene related to 'ETHNICITY'.

Table S26.  Basic characteristics of clinical feature: 'ETHNICITY'

ETHNICITY Labels N
  HISPANIC OR LATINO 25
  NOT HISPANIC OR LATINO 458
     
  Significant markers N = 0
Methods & Data
Input

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

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

  • Number of patients = 520

  • Number of genes = 18378

  • 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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