Correlation between mRNAseq expression and clinical features
Lung Squamous Cell Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1B857JW
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/C1B857JW
Overview
Introduction

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

Summary

Testing the association between 18514 genes and 15 clinical features across 501 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 'YEARS_TO_BIRTH'.

    • PRSS12|8492 ,  GLI3|2737 ,  CEP55|55165 ,  SFXN4|119559 ,  NT5C3L|115024 ,  ...

  • 30 genes correlated to 'PATHOLOGIC_STAGE'.

    • CA4|762 ,  CENPE|1062 ,  C8ORF46|254778 ,  VSIG2|23584 ,  TCOF1|6949 ,  ...

  • 30 genes correlated to 'PATHOLOGY_T_STAGE'.

    • SFTPC|6440 ,  C8ORF46|254778 ,  CLDN18|51208 ,  CA4|762 ,  ZBTB3|79842 ,  ...

  • 30 genes correlated to 'PATHOLOGY_N_STAGE'.

    • KPNA2|3838 ,  SMARCD2|6603 ,  CCNA2|890 ,  DEPDC1B|55789 ,  ASF1B|55723 ,  ...

  • 4 genes correlated to 'GENDER'.

    • CYORF15A|246126 ,  CYORF15B|84663 ,  HDHD1A|8226 ,  CLEC10A|10462

  • 30 genes correlated to 'KARNOFSKY_PERFORMANCE_SCORE'.

    • PPIAL4G|644591 ,  LOC90834|90834 ,  CEP290|80184 ,  ZNF468|90333 ,  UBB|7314 ,  ...

  • 30 genes correlated to 'HISTOLOGICAL_TYPE'.

    • ZNF512|84450 ,  TOPBP1|11073 ,  STAG1|10274 ,  C20ORF177|63939 ,  SNX4|8723 ,  ...

  • 30 genes correlated to 'YEAR_OF_TOBACCO_SMOKING_ONSET'.

    • DUS1L|64118 ,  C17ORF56|146705 ,  LOC146880|146880 ,  C16ORF79|283870 ,  QRICH2|84074 ,  ...

  • 18 genes correlated to 'RACE'.

    • LRRC37A2|474170 ,  C14ORF167|55449 ,  UTS2|10911 ,  PPIL3|53938 ,  FMO1|2326 ,  ...

  • No genes correlated to 'DAYS_TO_DEATH_OR_LAST_FUP', 'PATHOLOGY_M_STAGE', 'RADIATION_THERAPY', 'NUMBER_PACK_YEARS_SMOKED', 'RESIDUAL_TUMOR', 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=0        
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=1 lower stage N=29
PATHOLOGY_N_STAGE Spearman correlation test N=30 higher stage N=24 lower stage N=6
PATHOLOGY_M_STAGE Wilcoxon test   N=0        
GENDER Wilcoxon test N=4 male N=4 female N=0
RADIATION_THERAPY Wilcoxon test   N=0        
KARNOFSKY_PERFORMANCE_SCORE Spearman correlation test N=30 higher score N=24 lower score N=6
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=30 higher year_of_tobacco_smoking_onset N=25 lower year_of_tobacco_smoking_onset N=5
RESIDUAL_TUMOR Kruskal-Wallis test   N=0        
RACE Kruskal-Wallis test N=18        
ETHNICITY Wilcoxon test   N=0        
Clinical variable #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

No gene 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) 0-173.8 (median=21.9)
  censored N = 284
  death N = 216
     
  Significant markers N = 0
Clinical variable #2: 'YEARS_TO_BIRTH'

30 genes related to 'YEARS_TO_BIRTH'.

Table S2.  Basic characteristics of clinical feature: 'YEARS_TO_BIRTH'

YEARS_TO_BIRTH Mean (SD) 67.19 (8.6)
  Significant markers N = 30
  pos. correlated 19
  neg. correlated 11
List of top 10 genes differentially expressed by 'YEARS_TO_BIRTH'

Table S3.  Get Full Table List of top 10 genes significantly correlated to 'YEARS_TO_BIRTH' by Spearman correlation test

SpearmanCorr corrP Q
PRSS12|8492 0.2732 7.779e-10 1.44e-05
GLI3|2737 0.2559 8.869e-09 8.21e-05
CEP55|55165 -0.2422 5.53e-08 0.000341
SFXN4|119559 -0.233 1.763e-07 0.000483
NT5C3L|115024 -0.2327 1.848e-07 0.000483
NSUN5|55695 -0.2311 2.253e-07 0.000483
CENPA|1058 -0.2306 2.385e-07 0.000483
RHBDD1|84236 0.23 2.566e-07 0.000483
MMP10|4319 0.2301 2.607e-07 0.000483
GLB1L|79411 0.2299 2.61e-07 0.000483
Clinical variable #3: 'PATHOLOGIC_STAGE'

30 genes related to 'PATHOLOGIC_STAGE'.

Table S4.  Basic characteristics of clinical feature: 'PATHOLOGIC_STAGE'

PATHOLOGIC_STAGE Labels N
  STAGE I 3
  STAGE IA 90
  STAGE IB 151
  STAGE II 3
  STAGE IIA 65
  STAGE IIB 94
  STAGE III 3
  STAGE IIIA 63
  STAGE IIIB 18
  STAGE IV 7
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'PATHOLOGIC_STAGE'

Table S5.  Get Full Table List of top 10 genes differentially expressed by 'PATHOLOGIC_STAGE'

kruskal_wallis_P Q
CA4|762 2.137e-08 0.000396
CENPE|1062 4.824e-07 0.00447
C8ORF46|254778 1.454e-06 0.00897
VSIG2|23584 2.026e-06 0.00938
TCOF1|6949 3.281e-06 0.0121
TAF15|8148 4.464e-06 0.0132
TXNDC6|347736 5.001e-06 0.0132
PIGR|5284 7.391e-06 0.0143
CYP2B7P1|1556 7.746e-06 0.0143
CLDN18|51208 7.764e-06 0.0143
Clinical variable #4: 'PATHOLOGY_T_STAGE'

30 genes related to 'PATHOLOGY_T_STAGE'.

Table S6.  Basic characteristics of clinical feature: 'PATHOLOGY_T_STAGE'

PATHOLOGY_T_STAGE Mean (SD) 2.01 (0.74)
  N
  T1 114
  T2 293
  T3 71
  T4 23
     
  Significant markers N = 30
  pos. correlated 1
  neg. correlated 29
List of top 10 genes differentially expressed by 'PATHOLOGY_T_STAGE'

Table S7.  Get Full Table List of top 10 genes significantly correlated to 'PATHOLOGY_T_STAGE' by Spearman correlation test

SpearmanCorr corrP Q
SFTPC|6440 -0.2415 6.247e-08 0.00116
C8ORF46|254778 -0.2244 7.329e-07 0.00678
CLDN18|51208 -0.2102 2.289e-06 0.0111
CA4|762 -0.226 2.4e-06 0.0111
ZBTB3|79842 -0.2057 3.463e-06 0.0128
ADH1B|125 -0.2049 4.795e-06 0.0133
TNNC1|7134 -0.2037 5.024e-06 0.0133
GPR44|11251 -0.2009 6.093e-06 0.014
FIGF|2277 -0.2 7.169e-06 0.014
AGER|177 -0.1977 8.267e-06 0.014
Clinical variable #5: 'PATHOLOGY_N_STAGE'

30 genes related to 'PATHOLOGY_N_STAGE'.

Table S8.  Basic characteristics of clinical feature: 'PATHOLOGY_N_STAGE'

PATHOLOGY_N_STAGE Mean (SD) 0.46 (0.69)
  N
  N0 319
  N1 131
  N2 40
  N3 5
     
  Significant markers N = 30
  pos. correlated 24
  neg. correlated 6
List of top 10 genes differentially expressed by 'PATHOLOGY_N_STAGE'

Table S9.  Get Full Table List of top 10 genes significantly correlated to 'PATHOLOGY_N_STAGE' by Spearman correlation test

SpearmanCorr corrP Q
KPNA2|3838 0.2403 6.205e-08 0.00115
SMARCD2|6603 0.2265 3.521e-07 0.00298
CCNA2|890 0.2195 8.169e-07 0.00298
DEPDC1B|55789 0.2184 9.338e-07 0.00298
ASF1B|55723 0.2176 1.019e-06 0.00298
NEIL3|55247 0.2169 1.103e-06 0.00298
MND1|84057 0.2168 1.126e-06 0.00298
MRPL12|6182 0.2156 1.292e-06 0.00299
COX6A1|1337 0.2141 1.527e-06 0.00302
MRPL38|64978 0.2135 1.64e-06 0.00302
Clinical variable #6: 'PATHOLOGY_M_STAGE'

No gene related to 'PATHOLOGY_M_STAGE'.

Table S10.  Basic characteristics of clinical feature: 'PATHOLOGY_M_STAGE'

PATHOLOGY_M_STAGE Labels N
  class0 411
  class1 7
     
  Significant markers N = 0
Clinical variable #7: 'GENDER'

4 genes related to 'GENDER'.

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

GENDER Labels N
  FEMALE 130
  MALE 371
     
  Significant markers N = 4
  Higher in MALE 4
  Higher in FEMALE 0
List of 4 genes differentially expressed by 'GENDER'

Table S12.  Get Full Table List of 4 genes differentially expressed by 'GENDER'. 26 significant gene(s) located in sex chromosomes is(are) filtered out.

W(pos if higher in 'MALE') wilcoxontestP Q AUC
CYORF15A|246126 10736 4.165e-19 6.83e-16 0.9979
CYORF15B|84663 7766 1.839e-14 1.89e-11 0.9968
HDHD1A|8226 14301 6.02e-12 5.57e-09 0.7027
CLEC10A|10462 15897 7.242e-09 4.62e-06 0.6704
Clinical variable #8: 'RADIATION_THERAPY'

No gene related to 'RADIATION_THERAPY'.

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

RADIATION_THERAPY Labels N
  NO 384
  YES 53
     
  Significant markers N = 0
Clinical variable #9: 'KARNOFSKY_PERFORMANCE_SCORE'

30 genes related to 'KARNOFSKY_PERFORMANCE_SCORE'.

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

KARNOFSKY_PERFORMANCE_SCORE Mean (SD) 60.3 (41)
  Significant markers N = 30
  pos. correlated 24
  neg. correlated 6
List of top 10 genes differentially expressed by 'KARNOFSKY_PERFORMANCE_SCORE'

Table S15.  Get Full Table List of top 10 genes significantly correlated to 'KARNOFSKY_PERFORMANCE_SCORE' by Spearman correlation test

SpearmanCorr corrP Q
PPIAL4G|644591 -0.402 7.947e-08 0.00147
LOC90834|90834 0.375 6.977e-07 0.00445
CEP290|80184 0.3734 7.218e-07 0.00445
ZNF468|90333 -0.3669 1.162e-06 0.00538
UBB|7314 -0.3637 1.456e-06 0.00539
TUBGCP6|85378 0.358 2.19e-06 0.00676
DDX17|10521 0.3269 1.719e-05 0.0427
C15ORF28|80035 0.3305 2.23e-05 0.0427
PKD1|5310 0.3217 2.38e-05 0.0427
SPRN|503542 0.3212 2.455e-05 0.0427
Clinical variable #10: 'HISTOLOGICAL_TYPE'

30 genes related to 'HISTOLOGICAL_TYPE'.

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

HISTOLOGICAL_TYPE Labels N
  LUNG BASALOID SQUAMOUS CELL CARCINOMA 15
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA 6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) 479
     
  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
ZNF512|84450 2.087e-06 0.0386
TOPBP1|11073 1.453e-05 0.0996
STAG1|10274 2.131e-05 0.0996
C20ORF177|63939 2.51e-05 0.0996
SNX4|8723 3.505e-05 0.0996
MBTD1|54799 4.265e-05 0.0996
PRUNE|58497 4.3e-05 0.0996
AADAT|51166 4.617e-05 0.0996
PRDM1|639 5.001e-05 0.0996
SETDB1|9869 5.472e-05 0.0996
Clinical variable #11: 'NUMBER_PACK_YEARS_SMOKED'

No gene related to 'NUMBER_PACK_YEARS_SMOKED'.

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

NUMBER_PACK_YEARS_SMOKED Mean (SD) 52.69 (31)
  Significant markers N = 0
Clinical variable #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

30 genes related to 'YEAR_OF_TOBACCO_SMOKING_ONSET'.

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

YEAR_OF_TOBACCO_SMOKING_ONSET Mean (SD) 1960.61 (11)
  Significant markers N = 30
  pos. correlated 25
  neg. correlated 5
List of top 10 genes differentially expressed by 'YEAR_OF_TOBACCO_SMOKING_ONSET'

Table S20.  Get Full Table List of top 10 genes significantly correlated to 'YEAR_OF_TOBACCO_SMOKING_ONSET' by Spearman correlation test

SpearmanCorr corrP Q
DUS1L|64118 0.3086 1.911e-08 0.000167
C17ORF56|146705 0.3079 2.079e-08 0.000167
LOC146880|146880 0.3055 2.714e-08 0.000167
C16ORF79|283870 0.3 4.893e-08 0.000226
QRICH2|84074 0.2951 8.668e-08 0.000292
CCDC154|645811 0.3012 9.472e-08 0.000292
CTDSP2|10106 -0.2907 1.311e-07 0.000307
EME1|146956 0.2906 1.324e-07 0.000307
ZCCHC8|55596 0.2832 2.818e-07 0.000533
RNF208|727800 0.2819 3.189e-07 0.000533
Clinical variable #13: 'RESIDUAL_TUMOR'

No gene related to 'RESIDUAL_TUMOR'.

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

RESIDUAL_TUMOR Labels N
  R0 398
  R1 12
  R2 4
  RX 23
     
  Significant markers N = 0
Clinical variable #14: 'RACE'

18 genes related to 'RACE'.

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

RACE Labels N
  ASIAN 9
  BLACK OR AFRICAN AMERICAN 30
  WHITE 349
     
  Significant markers N = 18
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
LRRC37A2|474170 7.14e-06 0.0648
C14ORF167|55449 7.932e-06 0.0648
UTS2|10911 1.796e-05 0.0648
PPIL3|53938 2.012e-05 0.0648
FMO1|2326 2.094e-05 0.0648
POM121L10P|646074 2.134e-05 0.0648
LOC644172|644172 2.451e-05 0.0648
NAPEPLD|222236 5.276e-05 0.122
LOC388796|388796 6.538e-05 0.134
TOP1MT|116447 8.488e-05 0.157
Clinical variable #15: 'ETHNICITY'

No gene related to 'ETHNICITY'.

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

ETHNICITY Labels N
  HISPANIC OR LATINO 8
  NOT HISPANIC OR LATINO 316
     
  Significant markers N = 0
Methods & Data
Input

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

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

  • Number of patients = 501

  • Number of genes = 18514

  • Number of clinical features = 15

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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