Lung Adenocarcinoma: Correlation between mRNAseq expression and clinical features
Maintained by Juok Cho (Broad Institute)
Overview
Introduction

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

Summary

Testing the association between 18286 genes and 11 clinical features across 263 samples, statistically thresholded by Q value < 0.05, 7 clinical features related to at least one genes.

  • 10 genes correlated to 'Time to Death'.

    • ESYT3|83850 ,  UCN2|90226 ,  PPP1R3G|648791 ,  LYAR|55646 ,  MYLIP|29116 ,  ...

  • 32 genes correlated to 'GENDER'.

    • PRKY|5616 ,  ZFY|7544 ,  RPS4Y1|6192 ,  XIST|7503 ,  DDX3Y|8653 ,  ...

  • 8 genes correlated to 'HISTOLOGICAL.TYPE'.

    • TIGD2|166815 ,  A4GNT|51146 ,  DPCR1|135656 ,  MIA|8190 ,  CA2|760 ,  ...

  • 15 genes correlated to 'PATHOLOGY.T'.

    • RAB30|27314 ,  FAM125B|89853 ,  FAM46C|54855 ,  TTLL12|23170 ,  FCRLA|84824 ,  ...

  • 3 genes correlated to 'PATHOLOGY.N'.

    • RARS|5917 ,  ZNF483|158399 ,  FAM117A|81558

  • 6 genes correlated to 'PATHOLOGICSPREAD(M)'.

    • TMEM141|85014 ,  C19ORF10|56005 ,  STK16|8576 ,  NCRNA00116|205251 ,  CIB1|10519 ,  ...

  • 10 genes correlated to 'TUMOR.STAGE'.

    • ST6GAL1|6480 ,  FAM117A|81558 ,  AMPD1|270 ,  ZFP3|124961 ,  KIAA0125|9834 ,  ...

  • No genes correlated to 'AGE', 'KARNOFSKY.PERFORMANCE.SCORE', 'RADIATIONS.RADIATION.REGIMENINDICATION', and 'NEOADJUVANT.THERAPY'.

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 Q value < 0.05.

Clinical feature Statistical test Significant genes Associated with                 Associated with
Time to Death Cox regression test N=10 shorter survival N=6 longer survival N=4
AGE Spearman correlation test   N=0        
GENDER t test N=32 male N=15 female N=17
KARNOFSKY PERFORMANCE SCORE Spearman correlation test   N=0        
HISTOLOGICAL TYPE ANOVA test N=8        
PATHOLOGY T Spearman correlation test N=15 higher pT N=2 lower pT N=13
PATHOLOGY N Spearman correlation test N=3 higher pN N=1 lower pN N=2
PATHOLOGICSPREAD(M) ANOVA test N=6        
TUMOR STAGE Spearman correlation test N=10 higher stage N=1 lower stage N=9
RADIATIONS RADIATION REGIMENINDICATION t test   N=0        
NEOADJUVANT THERAPY t test   N=0        
Clinical variable #1: 'Time to Death'

10 genes related to 'Time to Death'.

Table S1.  Basic characteristics of clinical feature: 'Time to Death'

Time to Death Duration (Months) 0-224 (median=15)
  censored N = 152
  death N = 78
     
  Significant markers N = 10
  associated with shorter survival 6
  associated with longer survival 4
List of 10 genes significantly associated with 'Time to Death' by Cox regression test

Table S2.  Get Full Table List of 10 genes significantly associated with 'Time to Death' by Cox regression test

HazardRatio Wald_P Q C_index
ESYT3|83850 0.72 4.547e-08 0.00083 0.335
UCN2|90226 1.37 1.508e-07 0.0028 0.658
PPP1R3G|648791 1.57 5.972e-07 0.011 0.684
LYAR|55646 2.4 6.722e-07 0.012 0.666
MYLIP|29116 0.5 8.24e-07 0.015 0.337
MFSD2B|388931 1.72 1.091e-06 0.02 0.681
DKK1|22943 1.19 1.515e-06 0.028 0.713
B3GNT8|374907 0.71 1.846e-06 0.034 0.322
RGS20|8601 1.24 2.44e-06 0.045 0.672
BTG2|7832 0.63 2.471e-06 0.045 0.351

Figure S1.  Get High-res Image As an example, this figure shows the association of ESYT3|83850 to 'Time to Death'. four curves present the cumulative survival rates of 4 quartile subsets of patients. P value = 4.55e-08 with univariate Cox regression analysis using continuous log-2 expression values.

Clinical variable #2: 'AGE'

No gene related to 'AGE'.

Table S3.  Basic characteristics of clinical feature: 'AGE'

AGE Mean (SD) 65.38 (9.7)
  Significant markers N = 0
Clinical variable #3: 'GENDER'

32 genes related to 'GENDER'.

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

GENDER Labels N
  FEMALE 144
  MALE 119
     
  Significant markers N = 32
  Higher in MALE 15
  Higher in FEMALE 17
List of top 10 genes differentially expressed by 'GENDER'

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

T(pos if higher in 'MALE') ttestP Q AUC
PRKY|5616 38.85 1.111e-103 2.03e-99 0.9991
ZFY|7544 43.36 6.888e-76 1.26e-71 0.9973
RPS4Y1|6192 40.05 3.272e-65 5.98e-61 0.9952
XIST|7503 -32.38 8.331e-65 1.52e-60 0.9841
DDX3Y|8653 35.69 1.904e-42 3.48e-38 0.9963
NLGN4Y|22829 21.6 4.7e-34 8.59e-30 0.9894
TSIX|9383 -17.45 1.486e-30 2.72e-26 0.9891
USP9Y|8287 28.62 6.617e-28 1.21e-23 0.9997
KDM5D|8284 26.98 1.492e-25 2.73e-21 0.9968
ZRSR2|8233 -9.4 4.194e-18 7.66e-14 0.808

Figure S2.  Get High-res Image As an example, this figure shows the association of PRKY|5616 to 'GENDER'. P value = 1.11e-103 with T-test analysis.

Clinical variable #4: 'KARNOFSKY.PERFORMANCE.SCORE'

No gene related to 'KARNOFSKY.PERFORMANCE.SCORE'.

Table S6.  Basic characteristics of clinical feature: 'KARNOFSKY.PERFORMANCE.SCORE'

KARNOFSKY.PERFORMANCE.SCORE Mean (SD) 70.5 (38)
  Significant markers N = 0
Clinical variable #5: 'HISTOLOGICAL.TYPE'

8 genes related to 'HISTOLOGICAL.TYPE'.

Table S7.  Basic characteristics of clinical feature: 'HISTOLOGICAL.TYPE'

HISTOLOGICAL.TYPE Labels N
  LUNG ACINAR ADENOCARCINOMA 3
  LUNG ADENOCARCINOMA MIXED SUBTYPE 59
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) 170
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS 3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS 8
  LUNG CLEAR CELL ADENOCARCINOMA 2
  LUNG MICROPAPILLARY ADENOCARCINOMA 2
  LUNG MUCINOUS ADENOCARCINOMA 2
  LUNG PAPILLARY ADENOCARCINOMA 10
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA 1
  MUCINOUS (COLLOID) ADENOCARCINOMA 3
     
  Significant markers N = 8
List of 8 genes differentially expressed by 'HISTOLOGICAL.TYPE'

Table S8.  Get Full Table List of 8 genes differentially expressed by 'HISTOLOGICAL.TYPE'

ANOVA_P Q
TIGD2|166815 3.811e-08 0.000697
A4GNT|51146 9.007e-08 0.00165
DPCR1|135656 1.357e-07 0.00248
MIA|8190 2.727e-07 0.00499
CA2|760 3.91e-07 0.00715
GDPD2|54857 5.49e-07 0.01
ELOVL5|60481 7.573e-07 0.0138
SOX10|6663 2.635e-06 0.0482

Figure S3.  Get High-res Image As an example, this figure shows the association of TIGD2|166815 to 'HISTOLOGICAL.TYPE'. P value = 3.81e-08 with ANOVA analysis.

Clinical variable #6: 'PATHOLOGY.T'

15 genes related to 'PATHOLOGY.T'.

Table S9.  Basic characteristics of clinical feature: 'PATHOLOGY.T'

PATHOLOGY.T Mean (SD) 1.93 (0.74)
  N
  T1 68
  T2 159
  T3 21
  T4 14
     
  Significant markers N = 15
  pos. correlated 2
  neg. correlated 13
List of top 10 genes significantly correlated to 'PATHOLOGY.T' by Spearman correlation test

Table S10.  Get Full Table List of top 10 genes significantly correlated to 'PATHOLOGY.T' by Spearman correlation test

SpearmanCorr corrP Q
RAB30|27314 -0.3173 1.538e-07 0.00281
FAM125B|89853 -0.308 3.674e-07 0.00672
FAM46C|54855 -0.3073 3.887e-07 0.00711
TTLL12|23170 0.3017 6.476e-07 0.0118
FCRLA|84824 -0.3007 7.072e-07 0.0129
RGL1|23179 -0.2987 8.481e-07 0.0155
STAP1|26228 -0.2956 1.107e-06 0.0202
CD79A|973 -0.2945 1.219e-06 0.0223
CD19|930 -0.2955 1.231e-06 0.0225
ST8SIA1|6489 -0.2913 1.616e-06 0.0295

Figure S4.  Get High-res Image As an example, this figure shows the association of RAB30|27314 to 'PATHOLOGY.T'. P value = 1.54e-07 with Spearman correlation analysis.

Clinical variable #7: 'PATHOLOGY.N'

3 genes related to 'PATHOLOGY.N'.

Table S11.  Basic characteristics of clinical feature: 'PATHOLOGY.N'

PATHOLOGY.N Mean (SD) 0.6 (0.8)
  N
  N0 152
  N1 56
  N2 48
  N3 1
     
  Significant markers N = 3
  pos. correlated 1
  neg. correlated 2
List of 3 genes significantly correlated to 'PATHOLOGY.N' by Spearman correlation test

Table S12.  Get Full Table List of 3 genes significantly correlated to 'PATHOLOGY.N' by Spearman correlation test

SpearmanCorr corrP Q
RARS|5917 0.3318 5.063e-08 0.000926
ZNF483|158399 -0.2929 1.77e-06 0.0324
FAM117A|81558 -0.2891 2.431e-06 0.0445

Figure S5.  Get High-res Image As an example, this figure shows the association of RARS|5917 to 'PATHOLOGY.N'. P value = 5.06e-08 with Spearman correlation analysis.

Clinical variable #8: 'PATHOLOGICSPREAD(M)'

6 genes related to 'PATHOLOGICSPREAD(M)'.

Table S13.  Basic characteristics of clinical feature: 'PATHOLOGICSPREAD(M)'

PATHOLOGICSPREAD(M) Labels N
  M0 192
  M1 15
  MX 49
     
  Significant markers N = 6
List of 6 genes differentially expressed by 'PATHOLOGICSPREAD(M)'

Table S14.  Get Full Table List of 6 genes differentially expressed by 'PATHOLOGICSPREAD(M)'

ANOVA_P Q
TMEM141|85014 1.297e-06 0.0237
C19ORF10|56005 1.646e-06 0.0301
STK16|8576 1.738e-06 0.0318
NCRNA00116|205251 1.895e-06 0.0346
CIB1|10519 2.209e-06 0.0404
MLL5|55904 2.557e-06 0.0467

Figure S6.  Get High-res Image As an example, this figure shows the association of TMEM141|85014 to 'PATHOLOGICSPREAD(M)'. P value = 1.3e-06 with ANOVA analysis.

Clinical variable #9: 'TUMOR.STAGE'

10 genes related to 'TUMOR.STAGE'.

Table S15.  Basic characteristics of clinical feature: 'TUMOR.STAGE'

TUMOR.STAGE Mean (SD) 1.8 (0.95)
  N
  Stage 1 134
  Stage 2 56
  Stage 3 54
  Stage 4 14
     
  Significant markers N = 10
  pos. correlated 1
  neg. correlated 9
List of 10 genes significantly correlated to 'TUMOR.STAGE' by Spearman correlation test

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

SpearmanCorr corrP Q
ST6GAL1|6480 -0.3181 1.781e-07 0.00326
FAM117A|81558 -0.3157 2.231e-07 0.00408
AMPD1|270 -0.3182 3.83e-07 0.007
ZFP3|124961 -0.3049 5.964e-07 0.0109
KIAA0125|9834 -0.2983 1.119e-06 0.0205
RARS|5917 0.2923 1.783e-06 0.0326
ZNF540|163255 -0.2921 1.815e-06 0.0332
POU2AF1|5450 -0.29 2.169e-06 0.0396
STAP1|26228 -0.2899 2.187e-06 0.04
RNASE1|6035 -0.2889 2.376e-06 0.0434

Figure S7.  Get High-res Image As an example, this figure shows the association of ST6GAL1|6480 to 'TUMOR.STAGE'. P value = 1.78e-07 with Spearman correlation analysis.

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 17
  YES 246
     
  Significant markers N = 0
Clinical variable #11: 'NEOADJUVANT.THERAPY'

No gene related to 'NEOADJUVANT.THERAPY'.

Table S18.  Basic characteristics of clinical feature: 'NEOADJUVANT.THERAPY'

NEOADJUVANT.THERAPY Labels N
  NO 41
  YES 222
     
  Significant markers N = 0
Methods & Data
Input

  • Expresson data file = LUAD.uncv2.mRNAseq_RSEM_normalized_log2.txt

  • Clinical data file = LUAD.clin.merged.picked.txt

  • Number of patients = 263

  • Number of genes = 18286

  • Number of clinical features = 11

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

Student's t-test analysis

For two-class clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the log2-expression levels between the two clinical classes using 't.test' function in R

ANOVA analysis

For multi-class clinical features (ordinal or nominal), one-way analysis of variance (Howell 2002) was applied to compare the log2-expression levels between different clinical classes using 'anova' function in R

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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[4] Howell, D, Statistical Methods for Psychology. (5th ed.), Duxbury Press:324-5 (2002)
[5] 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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