Correlation between mRNAseq expression and clinical features
Lung Squamous Cell Carcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C14M93KS
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/C14M93KS
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 492 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 ,  GLB1L|79411 ,  SFXN4|119559 ,  CEP55|55165 ,  ...

  • 30 genes correlated to 'NEOPLASM_DISEASESTAGE'.

    • CA4|762 ,  CENPE|1062 ,  TCOF1|6949 ,  TAF15|8148 ,  C8ORF46|254778 ,  ...

  • 30 genes correlated to 'PATHOLOGY_T_STAGE'.

    • SFTPC|6440 ,  C8ORF46|254778 ,  GDF10|2662 ,  CA4|762 ,  KLF15|28999 ,  ...

  • 30 genes correlated to 'PATHOLOGY_N_STAGE'.

    • KPNA2|3838 ,  CCNA2|890 ,  MRPL38|64978 ,  COX6A1|1337 ,  SMARCD2|6603 ,  ...

  • 4 genes correlated to 'GENDER'.

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

  • 30 genes correlated to 'KARNOFSKY_PERFORMANCE_SCORE'.

    • C16ORF79|283870 ,  LOC90834|90834 ,  PPIAL4G|644591 ,  LOC146880|146880 ,  NACA2|342538 ,  ...

  • 30 genes correlated to 'HISTOLOGICAL_TYPE'.

    • ZNF512|84450 ,  AADAT|51166 ,  TOPBP1|11073 ,  STAG1|10274 ,  TMPO|7112 ,  ...

  • 30 genes correlated to 'YEAR_OF_TOBACCO_SMOKING_ONSET'.

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

  • 19 genes correlated to 'RACE'.

    • C14ORF167|55449 ,  LRRC37A2|474170 ,  UTS2|10911 ,  POM121L10P|646074 ,  FMO1|2326 ,  ...

  • No genes correlated to 'DAYS_TO_DEATH_OR_LAST_FUP', 'PATHOLOGY_M_STAGE', 'RADIATIONS_RADIATION_REGIMENINDICATION', 'NUMBER_PACK_YEARS_SMOKED', 'COMPLETENESS_OF_RESECTION', 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=20 younger N=10
NEOPLASM_DISEASESTAGE 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=21 lower stage N=9
PATHOLOGY_M_STAGE Wilcoxon test   N=0        
GENDER Wilcoxon test N=4 male N=4 female N=0
KARNOFSKY_PERFORMANCE_SCORE Spearman correlation test N=30 higher score N=28 lower score N=2
HISTOLOGICAL_TYPE Kruskal-Wallis test N=30        
RADIATIONS_RADIATION_REGIMENINDICATION Wilcoxon test   N=0        
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
COMPLETENESS_OF_RESECTION Kruskal-Wallis test   N=0        
RACE Kruskal-Wallis test N=19        
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) 0-174.1 (median=19.1)
  censored N = 295
  death N = 196
     
  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) 67.26 (8.5)
  Significant markers N = 30
  pos. correlated 20
  neg. correlated 10
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 0.2779 5.375e-10 9.95e-06
GLI3|2737 0.2617 5.27e-09 4.88e-05
GLB1L|79411 0.2382 1.171e-07 0.000553
SFXN4|119559 -0.238 1.195e-07 0.000553
CEP55|55165 -0.2332 2.18e-07 0.000807
NT5C3L|115024 -0.2314 2.7e-07 0.000833
NCKAP5|344148 0.2242 6.416e-07 0.00139
MMP10|4319 0.2243 6.535e-07 0.00139
CENPA|1058 -0.2238 6.734e-07 0.00139
NWD1|284434 0.2253 8.45e-07 0.00156
Clinical variable #3: 'NEOPLASM_DISEASESTAGE'

30 genes related to 'NEOPLASM_DISEASESTAGE'.

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

NEOPLASM_DISEASESTAGE Labels N
  STAGE I 3
  STAGE IA 88
  STAGE IB 150
  STAGE II 2
  STAGE IIA 63
  STAGE IIB 91
  STAGE III 3
  STAGE IIIA 62
  STAGE IIIB 20
  STAGE IV 7
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'NEOPLASM_DISEASESTAGE'

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

kruskal_wallis_P Q
CA4|762 1.108e-07 0.00205
CENPE|1062 9.64e-07 0.00652
TCOF1|6949 1.192e-06 0.00652
TAF15|8148 1.408e-06 0.00652
C8ORF46|254778 5.483e-06 0.017
RPTOR|57521 5.705e-06 0.017
BDNFOS|497258 6.437e-06 0.017
TXNDC6|347736 7.43e-06 0.0172
CLDN18|51208 1.214e-05 0.025
MED24|9862 2.194e-05 0.0401
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 113
  T2 288
  T3 69
  T4 22
     
  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 -0.2338 2.154e-07 0.00399
C8ORF46|254778 -0.2271 6.484e-07 0.006
GDF10|2662 -0.2154 2.493e-06 0.0154
CA4|762 -0.2247 3.412e-06 0.0158
KLF15|28999 -0.2043 4.898e-06 0.0163
CLDN18|51208 -0.2042 5.424e-06 0.0163
CRYM|1428 -0.2032 7.076e-06 0.0163
ADH1B|125 -0.2019 8.07e-06 0.0163
FIGF|2277 -0.2003 8.429e-06 0.0163
GPR44|11251 -0.1985 9.517e-06 0.0163
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 313
  N1 129
  N2 39
  N3 5
     
  Significant markers N = 30
  pos. correlated 21
  neg. correlated 9
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 0.2352 1.557e-07 0.00288
CCNA2|890 0.2181 1.213e-06 0.00457
MRPL38|64978 0.218 1.224e-06 0.00457
COX6A1|1337 0.2179 1.234e-06 0.00457
SMARCD2|6603 0.2153 1.662e-06 0.00457
NEIL3|55247 0.2148 1.753e-06 0.00457
DEPDC1B|55789 0.2135 2.046e-06 0.00457
DYNC2H1|79659 -0.2131 2.13e-06 0.00457
TK1|7083 0.212 2.406e-06 0.00457
MRPL12|6182 0.2107 2.781e-06 0.00457
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 403
  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 127
  MALE 365
     
  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 10198 1.598e-18 2.62e-15 0.9978
CYORF15B|84663 7275 7.45e-14 7.26e-11 0.9966
HDHD1A|8226 13523 3.256e-12 2.87e-09 0.7075
CXORF38|159013 14893 1.939e-09 1.2e-06 0.6787
Clinical variable #8: 'KARNOFSKY_PERFORMANCE_SCORE'

30 genes related to 'KARNOFSKY_PERFORMANCE_SCORE'.

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

KARNOFSKY_PERFORMANCE_SCORE Mean (SD) 56.35 (41)
  Significant markers N = 30
  pos. correlated 28
  neg. correlated 2
List of top 10 genes differentially expressed by 'KARNOFSKY_PERFORMANCE_SCORE'

Table S14.  Get Full Table List of top 10 genes significantly correlated to 'KARNOFSKY_PERFORMANCE_SCORE' by Spearman correlation test

SpearmanCorr corrP Q
C16ORF79|283870 0.5277 8.634e-09 0.00016
LOC90834|90834 0.518 2.1e-08 0.000194
PPIAL4G|644591 -0.5102 3.156e-08 0.000195
LOC146880|146880 0.4987 7.129e-08 0.000307
NACA2|342538 0.4966 8.28e-08 0.000307
NKTR|4820 0.4813 2.316e-07 0.000627
NPIPL3|23117 0.4798 2.556e-07 0.000627
SULT1A3|6818 0.4789 2.711e-07 0.000627
NEAT1|283131 0.4758 3.324e-07 0.000668
LUC7L3|51747 0.4745 3.609e-07 0.000668
Clinical variable #9: 'HISTOLOGICAL_TYPE'

30 genes related to 'HISTOLOGICAL_TYPE'.

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

HISTOLOGICAL_TYPE Labels N
  LUNG BASALOID SQUAMOUS CELL CARCINOMA 15
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA 1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA 6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) 469
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'HISTOLOGICAL_TYPE'

Table S16.  Get Full Table List of top 10 genes differentially expressed by 'HISTOLOGICAL_TYPE'

kruskal_wallis_P Q
ZNF512|84450 4.953e-06 0.0917
AADAT|51166 3.833e-05 0.161
TOPBP1|11073 3.931e-05 0.161
STAG1|10274 4.029e-05 0.161
TMPO|7112 5.513e-05 0.161
C20ORF177|63939 6.6e-05 0.161
PRUNE|58497 6.77e-05 0.161
MBTD1|54799 6.955e-05 0.161
CBX1|10951 9.714e-05 0.176
SNX4|8723 9.938e-05 0.176
Clinical variable #10: 'RADIATIONS_RADIATION_REGIMENINDICATION'

No gene related to 'RADIATIONS_RADIATION_REGIMENINDICATION'.

Table S17.  Basic characteristics of clinical feature: 'RADIATIONS_RADIATION_REGIMENINDICATION'

RADIATIONS_RADIATION_REGIMENINDICATION Labels N
  NO 13
  YES 479
     
  Significant markers N = 0
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) 52.64 (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) 1960.63 (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
C17ORF56|146705 0.3098 1.86e-08 0.000157
LOC146880|146880 0.3086 2.12e-08 0.000157
DUS1L|64118 0.307 2.546e-08 0.000157
C16ORF79|283870 0.2992 5.878e-08 0.00024
QRICH2|84074 0.2977 7.213e-08 0.00024
CCDC154|645811 0.304 7.791e-08 0.00024
CTDSP2|10106 -0.2944 9.77e-08 0.000258
SULT1A3|6818 0.2926 1.176e-07 0.000272
EME1|146956 0.2894 1.63e-07 0.000335
RNF208|727800 0.2866 2.165e-07 0.000401
Clinical variable #13: 'COMPLETENESS_OF_RESECTION'

No gene related to 'COMPLETENESS_OF_RESECTION'.

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

COMPLETENESS_OF_RESECTION Labels N
  R0 393
  R1 12
  R2 4
  RX 22
     
  Significant markers N = 0
Clinical variable #14: 'RACE'

19 genes related to 'RACE'.

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

RACE Labels N
  ASIAN 9
  BLACK OR AFRICAN AMERICAN 30
  WHITE 339
     
  Significant markers N = 19
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 6.158e-06 0.0653
LRRC37A2|474170 7.32e-06 0.0653
UTS2|10911 1.673e-05 0.0653
POM121L10P|646074 1.743e-05 0.0653
FMO1|2326 1.763e-05 0.0653
PPIL3|53938 2.371e-05 0.0732
LOC644172|644172 3.461e-05 0.0915
NAPEPLD|222236 4.805e-05 0.111
LOC388796|388796 6.168e-05 0.127
TOP1MT|116447 7.912e-05 0.146
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 307
     
  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 = 492

  • Number of genes = 18514

  • Number of clinical features = 15

Selected clinical features

  • For clinical features selected for this analysis and their value conozzle.versions, please find a documentation on selected CDEs .

  • 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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