Correlation between mRNAseq expression and clinical features
Lung Squamous Cell Carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C12R3QWR
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between mRNAseq expression and clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C12R3QWR
Overview
Introduction

This pipeline uses various statistical tests to identify mRNAs whose log2 expression levels correlated to selected clinical features.

Summary

Testing the association between 18514 genes and 15 clinical features across 499 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 ,  GLB1L|79411 ,  MMP10|4319 ,  ...

  • 30 genes correlated to 'PATHOLOGIC_STAGE'.

    • CA4|762 ,  CENPE|1062 ,  TXNDC6|347736 ,  C8ORF46|254778 ,  VSIG2|23584 ,  ...

  • 30 genes correlated to 'PATHOLOGY_T_STAGE'.

    • SFTPC|6440 ,  C8ORF46|254778 ,  CA4|762 ,  CLDN18|51208 ,  TNNC1|7134 ,  ...

  • 30 genes correlated to 'PATHOLOGY_N_STAGE'.

    • KPNA2|3838 ,  SMARCD2|6603 ,  ASF1B|55723 ,  COX6A1|1337 ,  DYNC2H1|79659 ,  ...

  • 4 genes correlated to 'GENDER'.

    • CYORF15A|246126 ,  CYORF15B|84663 ,  HDHD1A|8226 ,  CXORF38|159013

  • 30 genes correlated to 'KARNOFSKY_PERFORMANCE_SCORE'.

    • PPIAL4G|644591 ,  CEP290|80184 ,  LOC90834|90834 ,  ZNF468|90333 ,  TUBGCP6|85378 ,  ...

  • 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'.

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

  • 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=21 lower score N=9
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=21.1)
  censored N = 286
  death N = 212
     
  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) 67.22 (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 0.2792 3.325e-10 6.16e-06
GLI3|2737 0.2592 5.815e-09 5.38e-05
CEP55|55165 -0.2411 6.516e-08 0.000402
GLB1L|79411 0.2341 1.591e-07 0.000601
MMP10|4319 0.2342 1.624e-07 0.000601
SFXN4|119559 -0.2304 2.511e-07 0.000643
NT5C3L|115024 -0.2303 2.559e-07 0.000643
NSUN5|55695 -0.2289 3.024e-07 0.000643
CENPA|1058 -0.2286 3.126e-07 0.000643
RHBDD1|84236 0.2263 4.155e-07 0.000732
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 66
  STAGE IIB 93
  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 1.616e-08 0.000299
CENPE|1062 5.37e-07 0.00497
TXNDC6|347736 2.56e-06 0.0125
C8ORF46|254778 3.089e-06 0.0125
VSIG2|23584 4.224e-06 0.0125
TCOF1|6949 4.438e-06 0.0125
TAF15|8148 5.415e-06 0.0125
SSTR1|6751 5.419e-06 0.0125
CYP2B7P1|1556 7.988e-06 0.0141
CLDN18|51208 8.328e-06 0.0141
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 (0.74)
  N
  T1 114
  T2 292
  T3 70
  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 -0.2386 9.607e-08 0.00178
C8ORF46|254778 -0.2224 9.777e-07 0.00905
CA4|762 -0.2261 2.436e-06 0.015
CLDN18|51208 -0.2064 3.64e-06 0.0156
TNNC1|7134 -0.2035 5.344e-06 0.0156
ZBTB3|79842 -0.2017 5.566e-06 0.0156
ADH1B|125 -0.201 7.694e-06 0.0156
SMAD6|4091 -0.1975 8.847e-06 0.0156
FIGF|2277 -0.1982 9.085e-06 0.0156
GPR44|11251 -0.1971 9.606e-06 0.0156
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 318
  N1 130
  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 0.2381 8.777e-08 0.00162
SMARCD2|6603 0.2252 4.373e-07 0.00294
ASF1B|55723 0.218 1.022e-06 0.00294
COX6A1|1337 0.2171 1.137e-06 0.00294
DYNC2H1|79659 -0.2168 1.184e-06 0.00294
MRPL12|6182 0.2165 1.224e-06 0.00294
CCNA2|890 0.2158 1.322e-06 0.00294
DEPDC1B|55789 0.2153 1.405e-06 0.00294
MND1|84057 0.2145 1.533e-06 0.00294
NEIL3|55247 0.2142 1.59e-06 0.00294
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 407
  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 129
  MALE 370
     
  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 10708 4.14e-19 6.97e-16 0.9979
CYORF15B|84663 7745 1.849e-14 1.9e-11 0.9968
HDHD1A|8226 13969 2.796e-12 2.59e-09 0.7065
CXORF38|159013 15583 4.294e-09 2.65e-06 0.6735
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 370
  YES 49
     
  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) 60.62 (41)
  Significant markers N = 30
  pos. correlated 21
  neg. correlated 9
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 -0.3999 1.347e-07 0.00249
CEP290|80184 0.3722 1.081e-06 0.01
LOC90834|90834 0.3563 3.504e-06 0.0162
ZNF468|90333 -0.355 3.57e-06 0.0162
TUBGCP6|85378 0.3514 4.55e-06 0.0162
UBB|7314 -0.3492 5.253e-06 0.0162
CCDC88B|283234 0.3178 3.772e-05 0.0735
ATP5F1|515 -0.3175 3.842e-05 0.0735
C15ORF28|80035 0.325 3.907e-05 0.0735
PKD1|5310 0.3169 3.969e-05 0.0735
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) 477
     
  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 2.114e-06 0.0391
TOPBP1|11073 1.252e-05 0.0953
STAG1|10274 2.085e-05 0.0953
C20ORF177|63939 2.471e-05 0.0953
SNX4|8723 3.506e-05 0.0953
MBTD1|54799 4.232e-05 0.0953
PRUNE|58497 4.44e-05 0.0953
AADAT|51166 4.51e-05 0.0953
PRDM1|639 5.079e-05 0.0953
SETDB1|9869 5.526e-05 0.0953
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) 52.76 (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 397
  R1 12
  R2 4
  RX 22
     
  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 348
     
  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
C14ORF167|55449 7.637e-06 0.0678
LRRC37A2|474170 7.668e-06 0.0678
UTS2|10911 1.82e-05 0.0678
FMO1|2326 1.876e-05 0.0678
PPIL3|53938 2.079e-05 0.0678
POM121L10P|646074 2.196e-05 0.0678
LOC644172|644172 2.59e-05 0.0685
NAPEPLD|222236 5.261e-05 0.122
LOC388796|388796 6.206e-05 0.128
TOP1MT|116447 8.144e-05 0.151
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 315
     
  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 = 499

  • 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, Wald's test in univariate Cox regression analysis with proportional hazards model (Andersen and Gill 1982) was used to estimate the P values using the 'coxph' function in R. Kaplan-Meier survival curves were plot using the four quartile subgroups of patients based on expression levels

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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