Correlation between mRNAseq expression and clinical features
Thyroid Adenocarcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1PZ57HF
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between mRNAseq expression and clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1PZ57HF
Overview
Introduction

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

Summary

Testing the association between 17990 genes and 15 clinical features across 484 samples, statistically thresholded by Q value < 0.05, 13 clinical features related to at least one genes.

  • 86 genes correlated to 'AGE'.

    • ZNF518B|85460 ,  RANBP17|64901 ,  MSL3L2|151507 ,  HCG11|493812 ,  C12ORF52|84934 ,  ...

  • 660 genes correlated to 'NEOPLASM.DISEASESTAGE'.

    • GSPT2|23708 ,  SEMA3G|56920 ,  PIK3R3|8503 ,  FAM50B|26240 ,  SLC10A4|201780 ,  ...

  • 524 genes correlated to 'PATHOLOGY.T.STAGE'.

    • FBXO9|26268 ,  VIPR1|7433 ,  LTF|4057 ,  SPCS3|60559 ,  SLCO2A1|6578 ,  ...

  • 2604 genes correlated to 'PATHOLOGY.N.STAGE'.

    • CREB5|9586 ,  CLCNKA|1187 ,  FN1|2335 ,  SFTPB|6439 ,  MLEC|9761 ,  ...

  • 10 genes correlated to 'PATHOLOGY.M.STAGE'.

    • ST6GALNAC1|55808 ,  SELP|6403 ,  CYP21A2|1589 ,  C4ORF6|10141 ,  C19ORF76|199800 ,  ...

  • 44 genes correlated to 'GENDER'.

    • ZFY|7544 ,  RPS4Y1|6192 ,  DDX3Y|8653 ,  NLGN4Y|22829 ,  UTY|7404 ,  ...

  • 5461 genes correlated to 'HISTOLOGICAL.TYPE'.

    • TM7SF4|81501 ,  ITGA3|3675 ,  FN1|2335 ,  SFTPB|6439 ,  ERBB3|2065 ,  ...

  • 28 genes correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

    • C14ORF180|400258 ,  C4BPA|722 ,  FLJ37543|285668 ,  ENPP3|5169 ,  GPR142|350383 ,  ...

  • 6 genes correlated to 'RADIATIONEXPOSURE'.

    • CRNN|49860 ,  RNF17|56163 ,  CSNK1A1P|161635 ,  CYORF15A|246126 ,  EIF1AY|9086 ,  ...

  • 1053 genes correlated to 'EXTRATHYROIDAL.EXTENSION'.

    • ASAH2|56624 ,  SRPX2|27286 ,  SLC25A42|284439 ,  COL1A1|1277 ,  FAM69C|125704 ,  ...

  • 2 genes correlated to 'COMPLETENESS.OF.RESECTION'.

    • SHOX2|6474 ,  CATSPER2P1|440278

  • 1349 genes correlated to 'NUMBER.OF.LYMPH.NODES'.

    • PELI1|57162 ,  CBFB|865 ,  CREB5|9586 ,  FAM60A|58516 ,  CLCNKA|1187 ,  ...

  • 9 genes correlated to 'TUMOR.SIZE'.

    • C3ORF32|51066 ,  ISLR2|57611 ,  ZC3H10|84872 ,  LRRC55|219527 ,  SLC14A1|6563 ,  ...

  • No genes correlated to 'Time to Death', and 'MULTIFOCALITY'.

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=0        
AGE Spearman correlation test N=86 older N=37 younger N=49
NEOPLASM DISEASESTAGE ANOVA test N=660        
PATHOLOGY T STAGE Spearman correlation test N=524 higher stage N=108 lower stage N=416
PATHOLOGY N STAGE t test N=2604 class1 N=1242 class0 N=1362
PATHOLOGY M STAGE ANOVA test N=10        
GENDER t test N=44 male N=20 female N=24
HISTOLOGICAL TYPE ANOVA test N=5461        
RADIATIONS RADIATION REGIMENINDICATION t test N=28 yes N=16 no N=12
RADIATIONEXPOSURE t test N=6 yes N=3 no N=3
EXTRATHYROIDAL EXTENSION ANOVA test N=1053        
COMPLETENESS OF RESECTION ANOVA test N=2        
NUMBER OF LYMPH NODES Spearman correlation test N=1349 higher number.of.lymph.nodes N=725 lower number.of.lymph.nodes N=624
MULTIFOCALITY t test   N=0        
TUMOR SIZE Spearman correlation test N=9 higher tumor.size N=0 lower tumor.size N=9
Clinical variable #1: 'Time to Death'

No gene related to 'Time to Death'.

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

Time to Death Duration (Months) 0-158.8 (median=15.5)
  censored N = 466
  death N = 14
     
  Significant markers N = 0
Clinical variable #2: 'AGE'

86 genes related to 'AGE'.

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

AGE Mean (SD) 47.18 (16)
  Significant markers N = 86
  pos. correlated 37
  neg. correlated 49
List of top 10 genes significantly correlated to 'AGE' by Spearman correlation test

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

SpearmanCorr corrP Q
ZNF518B|85460 -0.3395 1.591e-14 2.86e-10
RANBP17|64901 -0.3308 9.533e-14 1.71e-09
MSL3L2|151507 -0.3201 5.427e-13 9.76e-09
HCG11|493812 -0.2908 6.89e-11 1.24e-06
C12ORF52|84934 0.2846 1.815e-10 3.27e-06
ASB13|79754 0.2806 3.284e-10 5.91e-06
DDIT4L|115265 0.2741 8.955e-10 1.61e-05
LHFPL4|375323 0.2847 9.612e-10 1.73e-05
IL20RA|53832 0.2737 9.89e-10 1.78e-05
ENTPD1|953 -0.2706 1.449e-09 2.61e-05

Figure S1.  Get High-res Image As an example, this figure shows the association of ZNF518B|85460 to 'AGE'. P value = 1.59e-14 with Spearman correlation analysis. The straight line presents the best linear regression.

Clinical variable #3: 'NEOPLASM.DISEASESTAGE'

660 genes related to 'NEOPLASM.DISEASESTAGE'.

Table S4.  Basic characteristics of clinical feature: 'NEOPLASM.DISEASESTAGE'

NEOPLASM.DISEASESTAGE Labels N
  STAGE I 274
  STAGE II 51
  STAGE III 105
  STAGE IV 2
  STAGE IVA 44
  STAGE IVC 6
     
  Significant markers N = 660
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'

ANOVA_P Q
GSPT2|23708 1.05e-14 1.89e-10
SEMA3G|56920 1.21e-13 2.18e-09
PIK3R3|8503 1.394e-13 2.51e-09
FAM50B|26240 1.826e-13 3.28e-09
SLC10A4|201780 4.378e-12 7.87e-08
CYP26A1|1592 6.056e-12 1.09e-07
DNASE1L3|1776 6.442e-12 1.16e-07
ITM2A|9452 6.674e-12 1.2e-07
ANXA3|306 2.296e-11 4.13e-07
ZNF518B|85460 4.847e-11 8.72e-07

Figure S2.  Get High-res Image As an example, this figure shows the association of GSPT2|23708 to 'NEOPLASM.DISEASESTAGE'. P value = 1.05e-14 with ANOVA analysis.

Clinical variable #4: 'PATHOLOGY.T.STAGE'

524 genes related to 'PATHOLOGY.T.STAGE'.

Table S6.  Basic characteristics of clinical feature: 'PATHOLOGY.T.STAGE'

PATHOLOGY.T.STAGE Mean (SD) 2.13 (0.88)
  N
  1 139
  2 161
  3 161
  4 21
     
  Significant markers N = 524
  pos. correlated 108
  neg. correlated 416
List of top 10 genes significantly correlated to 'PATHOLOGY.T.STAGE' by Spearman correlation test

Table S7.  Get Full Table List of top 10 genes significantly correlated to 'PATHOLOGY.T.STAGE' by Spearman correlation test

SpearmanCorr corrP Q
FBXO9|26268 -0.3114 2.696e-12 4.85e-08
VIPR1|7433 -0.3003 1.673e-11 3.01e-07
LTF|4057 -0.2899 8.737e-11 1.57e-06
SPCS3|60559 -0.2897 8.992e-11 1.62e-06
SLCO2A1|6578 -0.288 1.161e-10 2.09e-06
FAM65C|140876 -0.2829 2.525e-10 4.54e-06
SYT15|83849 -0.2828 2.562e-10 4.61e-06
GNG7|2788 -0.2824 2.724e-10 4.9e-06
LOC653566|653566 -0.2801 3.844e-10 6.91e-06
ITM2A|9452 -0.2772 5.984e-10 1.08e-05

Figure S3.  Get High-res Image As an example, this figure shows the association of FBXO9|26268 to 'PATHOLOGY.T.STAGE'. P value = 2.7e-12 with Spearman correlation analysis.

Clinical variable #5: 'PATHOLOGY.N.STAGE'

2604 genes related to 'PATHOLOGY.N.STAGE'.

Table S8.  Basic characteristics of clinical feature: 'PATHOLOGY.N.STAGE'

PATHOLOGY.N.STAGE Labels N
  class0 220
  class1 217
     
  Significant markers N = 2604
  Higher in class1 1242
  Higher in class0 1362
List of top 10 genes differentially expressed by 'PATHOLOGY.N.STAGE'

Table S9.  Get Full Table List of top 10 genes differentially expressed by 'PATHOLOGY.N.STAGE'

T(pos if higher in 'class1') ttestP Q AUC
CREB5|9586 9.7 4.389e-20 7.9e-16 0.7345
CLCNKA|1187 -9.6 8.149e-20 1.47e-15 0.7384
FN1|2335 9.4 4.99e-19 8.98e-15 0.7236
SFTPB|6439 9.31 1.565e-18 2.82e-14 0.7127
MLEC|9761 -9.22 2.161e-18 3.89e-14 0.7259
KCNN4|3783 9.14 3.885e-18 6.99e-14 0.7188
CBFB|865 9.09 5.904e-18 1.06e-13 0.7517
TMEM117|84216 8.95 1.11e-17 2e-13 0.7244
TMPRSS4|56649 8.97 1.616e-17 2.91e-13 0.7176
TMEM43|79188 8.9 2.374e-17 4.27e-13 0.7154

Figure S4.  Get High-res Image As an example, this figure shows the association of CREB5|9586 to 'PATHOLOGY.N.STAGE'. P value = 4.39e-20 with T-test analysis.

Clinical variable #6: 'PATHOLOGY.M.STAGE'

10 genes related to 'PATHOLOGY.M.STAGE'.

Table S10.  Basic characteristics of clinical feature: 'PATHOLOGY.M.STAGE'

PATHOLOGY.M.STAGE Labels N
  M0 265
  M1 9
  MX 209
     
  Significant markers N = 10
List of 10 genes differentially expressed by 'PATHOLOGY.M.STAGE'

Table S11.  Get Full Table List of 10 genes differentially expressed by 'PATHOLOGY.M.STAGE'

ANOVA_P Q
ST6GALNAC1|55808 1.112e-07 0.002
SELP|6403 1.734e-07 0.00312
CYP21A2|1589 1.763e-07 0.00317
C4ORF6|10141 2.152e-07 0.00387
C19ORF76|199800 5.236e-07 0.00942
APOL3|80833 1.074e-06 0.0193
GPATCH4|54865 1.075e-06 0.0193
KYNU|8942 1.258e-06 0.0226
EDN1|1906 1.813e-06 0.0326
SNRNP40|9410 2.739e-06 0.0493

Figure S5.  Get High-res Image As an example, this figure shows the association of ST6GALNAC1|55808 to 'PATHOLOGY.M.STAGE'. P value = 1.11e-07 with ANOVA analysis.

Clinical variable #7: 'GENDER'

44 genes related to 'GENDER'.

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

GENDER Labels N
  FEMALE 354
  MALE 130
     
  Significant markers N = 44
  Higher in MALE 20
  Higher in FEMALE 24
List of top 10 genes differentially expressed by 'GENDER'

Table S13.  Get Full Table List of top 10 genes differentially expressed by 'GENDER'

T(pos if higher in 'MALE') ttestP Q AUC
ZFY|7544 93.19 2.153e-202 3.87e-198 1
RPS4Y1|6192 89.41 4.025e-201 7.24e-197 1
DDX3Y|8653 99.65 1.656e-188 2.98e-184 1
NLGN4Y|22829 65.37 6.194e-156 1.11e-151 1
UTY|7404 92.76 1.94e-150 3.49e-146 1
PRKY|5616 42.26 1.28e-142 2.3e-138 0.9939
KDM5D|8284 84.19 8.44e-131 1.52e-126 1
USP9Y|8287 73.65 3.633e-126 6.53e-122 0.9999
XIST|7503 -48.66 4.609e-91 8.29e-87 0.9941
CYORF15A|246126 57.19 2.197e-62 3.95e-58 1

Figure S6.  Get High-res Image As an example, this figure shows the association of ZFY|7544 to 'GENDER'. P value = 2.15e-202 with T-test analysis.

Clinical variable #8: 'HISTOLOGICAL.TYPE'

5461 genes related to 'HISTOLOGICAL.TYPE'.

Table S14.  Basic characteristics of clinical feature: 'HISTOLOGICAL.TYPE'

HISTOLOGICAL.TYPE Labels N
  OTHER SPECIFY 9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL 342
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED) 99
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES) 34
     
  Significant markers N = 5461
List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'

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

ANOVA_P Q
TM7SF4|81501 3.476e-45 6.25e-41
ITGA3|3675 1.252e-44 2.25e-40
FN1|2335 2.428e-44 4.37e-40
SFTPB|6439 5.653e-43 1.02e-38
ERBB3|2065 1.009e-42 1.81e-38
KCNN4|3783 3.989e-42 7.17e-38
SERPINA1|5265 1.433e-41 2.58e-37
TMPRSS4|56649 1.914e-41 3.44e-37
STAC|6769 5.311e-41 9.55e-37
UNC5CL|222643 8.643e-41 1.55e-36

Figure S7.  Get High-res Image As an example, this figure shows the association of TM7SF4|81501 to 'HISTOLOGICAL.TYPE'. P value = 3.48e-45 with ANOVA analysis.

Clinical variable #9: 'RADIATIONS.RADIATION.REGIMENINDICATION'

28 genes related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

Table S16.  Basic characteristics of clinical feature: 'RADIATIONS.RADIATION.REGIMENINDICATION'

RADIATIONS.RADIATION.REGIMENINDICATION Labels N
  NO 14
  YES 470
     
  Significant markers N = 28
  Higher in YES 16
  Higher in NO 12
List of top 10 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

Table S17.  Get Full Table List of top 10 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

T(pos if higher in 'YES') ttestP Q AUC
C14ORF180|400258 14.13 6.359e-19 1.14e-14 0.8784
C4BPA|722 9.46 3.539e-14 6.35e-10 0.7477
FLJ37543|285668 14.29 9.025e-14 1.62e-09 0.8706
ENPP3|5169 10.16 1.725e-09 3.1e-05 0.8714
GPR142|350383 9.82 5.169e-08 0.000928 0.8518
CUL7|9820 -9.27 5.409e-08 0.000971 0.8901
HPR|3250 10.21 6.735e-08 0.00121 0.8869
ARHGEF18|23370 -8.04 7.58e-08 0.00136 0.7903
HCFC1|3054 -9.05 1.143e-07 0.00205 0.8929
CXORF48|54967 9.32 1.325e-07 0.00238 0.8434

Figure S8.  Get High-res Image As an example, this figure shows the association of C14ORF180|400258 to 'RADIATIONS.RADIATION.REGIMENINDICATION'. P value = 6.36e-19 with T-test analysis.

Clinical variable #10: 'RADIATIONEXPOSURE'

6 genes related to 'RADIATIONEXPOSURE'.

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

RADIATIONEXPOSURE Labels N
  NO 407
  YES 17
     
  Significant markers N = 6
  Higher in YES 3
  Higher in NO 3
List of 6 genes differentially expressed by 'RADIATIONEXPOSURE'

Table S19.  Get Full Table List of 6 genes differentially expressed by 'RADIATIONEXPOSURE'

T(pos if higher in 'YES') ttestP Q AUC
CRNN|49860 -11.42 2.184e-13 3.93e-09 0.9138
RNF17|56163 -8.51 2.74e-13 4.93e-09 0.8733
CSNK1A1P|161635 -8.17 7.821e-13 1.41e-08 0.8206
CYORF15A|246126 7.04 7.06e-11 1.27e-06 0.6366
EIF1AY|9086 5.76 5.632e-08 0.00101 0.757
TTTY15|64595 5.43 5.453e-07 0.0098 0.7244

Figure S9.  Get High-res Image As an example, this figure shows the association of CRNN|49860 to 'RADIATIONEXPOSURE'. P value = 2.18e-13 with T-test analysis.

Clinical variable #11: 'EXTRATHYROIDAL.EXTENSION'

1053 genes related to 'EXTRATHYROIDAL.EXTENSION'.

Table S20.  Basic characteristics of clinical feature: 'EXTRATHYROIDAL.EXTENSION'

EXTRATHYROIDAL.EXTENSION Labels N
  MINIMAL (T3) 127
  MODERATE/ADVANCED (T4A) 16
  NONE 323
  VERY ADVANCED (T4B) 1
     
  Significant markers N = 1053
List of top 10 genes differentially expressed by 'EXTRATHYROIDAL.EXTENSION'

Table S21.  Get Full Table List of top 10 genes differentially expressed by 'EXTRATHYROIDAL.EXTENSION'

ANOVA_P Q
ASAH2|56624 1.441e-15 2.59e-11
SRPX2|27286 2.962e-15 5.33e-11
SLC25A42|284439 5.257e-15 9.46e-11
COL1A1|1277 1.818e-14 3.27e-10
FAM69C|125704 1.904e-14 3.42e-10
SLC10A4|201780 2.908e-14 5.23e-10
COL3A1|1281 4.798e-14 8.63e-10
POSTN|10631 5.86e-14 1.05e-09
FLJ42875|440556 8.248e-14 1.48e-09
CYP26A1|1592 1.231e-13 2.21e-09

Figure S10.  Get High-res Image As an example, this figure shows the association of ASAH2|56624 to 'EXTRATHYROIDAL.EXTENSION'. P value = 1.44e-15 with ANOVA analysis.

Clinical variable #12: 'COMPLETENESS.OF.RESECTION'

2 genes related to 'COMPLETENESS.OF.RESECTION'.

Table S22.  Basic characteristics of clinical feature: 'COMPLETENESS.OF.RESECTION'

COMPLETENESS.OF.RESECTION Labels N
  R0 371
  R1 49
  R2 4
  RX 29
     
  Significant markers N = 2
List of 2 genes differentially expressed by 'COMPLETENESS.OF.RESECTION'

Table S23.  Get Full Table List of 2 genes differentially expressed by 'COMPLETENESS.OF.RESECTION'

ANOVA_P Q
SHOX2|6474 1.243e-07 0.00224
CATSPER2P1|440278 4.83e-07 0.00869

Figure S11.  Get High-res Image As an example, this figure shows the association of SHOX2|6474 to 'COMPLETENESS.OF.RESECTION'. P value = 1.24e-07 with ANOVA analysis.

Clinical variable #13: 'NUMBER.OF.LYMPH.NODES'

1349 genes related to 'NUMBER.OF.LYMPH.NODES'.

Table S24.  Basic characteristics of clinical feature: 'NUMBER.OF.LYMPH.NODES'

NUMBER.OF.LYMPH.NODES Mean (SD) 3.55 (6.2)
  Significant markers N = 1349
  pos. correlated 725
  neg. correlated 624
List of top 10 genes significantly correlated to 'NUMBER.OF.LYMPH.NODES' by Spearman correlation test

Table S25.  Get Full Table List of top 10 genes significantly correlated to 'NUMBER.OF.LYMPH.NODES' by Spearman correlation test

SpearmanCorr corrP Q
PELI1|57162 0.395 8.647e-16 1.56e-11
CBFB|865 0.3935 1.139e-15 2.05e-11
CREB5|9586 0.3884 2.804e-15 5.04e-11
FAM60A|58516 0.3854 4.777e-15 8.59e-11
CLCNKA|1187 -0.3854 4.822e-15 8.67e-11
TAGLN2|8407 0.3789 1.488e-14 2.68e-10
GPR153|387509 0.3738 3.511e-14 6.31e-10
S100A10|6281 0.372 4.744e-14 8.53e-10
FECH|2235 -0.37 6.699e-14 1.2e-09
GPER|2852 -0.3653 1.441e-13 2.59e-09

Figure S12.  Get High-res Image As an example, this figure shows the association of PELI1|57162 to 'NUMBER.OF.LYMPH.NODES'. P value = 8.65e-16 with Spearman correlation analysis. The straight line presents the best linear regression.

Clinical variable #14: 'MULTIFOCALITY'

No gene related to 'MULTIFOCALITY'.

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

MULTIFOCALITY Labels N
  MULTIFOCAL 219
  UNIFOCAL 255
     
  Significant markers N = 0
Clinical variable #15: 'TUMOR.SIZE'

9 genes related to 'TUMOR.SIZE'.

Table S27.  Basic characteristics of clinical feature: 'TUMOR.SIZE'

TUMOR.SIZE Mean (SD) 2.96 (1.6)
  Significant markers N = 9
  pos. correlated 0
  neg. correlated 9
List of 9 genes significantly correlated to 'TUMOR.SIZE' by Spearman correlation test

Table S28.  Get Full Table List of 9 genes significantly correlated to 'TUMOR.SIZE' by Spearman correlation test

SpearmanCorr corrP Q
C3ORF32|51066 -0.2829 2.494e-08 0.000449
ISLR2|57611 -0.2721 5.593e-08 0.00101
ZC3H10|84872 -0.2607 2.032e-07 0.00366
LRRC55|219527 -0.2545 4.61e-07 0.00829
SLC14A1|6563 -0.2495 6.889e-07 0.0124
CLDN2|9075 -0.2471 1.012e-06 0.0182
CXCL12|6387 -0.2456 1.036e-06 0.0186
FOXI2|399823 -0.2443 1.43e-06 0.0257
APLNR|187 -0.2417 1.551e-06 0.0279

Figure S13.  Get High-res Image As an example, this figure shows the association of C3ORF32|51066 to 'TUMOR.SIZE'. P value = 2.49e-08 with Spearman correlation analysis. The straight line presents the best linear regression.

Methods & Data
Input

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

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

  • Number of patients = 484

  • Number of genes = 17990

  • Number of clinical features = 15

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

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

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

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