Correlation between mRNAseq expression and clinical features
Lung Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1NV9HP5
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/C1NV9HP5
Overview
Introduction

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

Summary

Testing the association between 18319 genes and 15 clinical features across 515 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 13 clinical features related to at least one genes.

  • 30 genes correlated to 'DAYS_TO_DEATH_OR_LAST_FUP'.

    • IRX5|10265 ,  MYO1E|4643 ,  DKK1|22943 ,  FAM83B|222584 ,  GNMT|27232 ,  ...

  • 30 genes correlated to 'YEARS_TO_BIRTH'.

    • GPR15|2838 ,  SLC40A1|30061 ,  C9ORF140|89958 ,  C7ORF68|29923 ,  EDA2R|60401 ,  ...

  • 30 genes correlated to 'PATHOLOGIC_STAGE'.

    • RASGRP2|10235 ,  PTGDS|5730 ,  FAM117A|81558 ,  BLK|640 ,  FAM125B|89853 ,  ...

  • 30 genes correlated to 'PATHOLOGY_T_STAGE'.

    • FAM125B|89853 ,  C14ORF139|79686 ,  RASGRP2|10235 ,  GP1BA|2811 ,  PTGDS|5730 ,  ...

  • 30 genes correlated to 'PATHOLOGY_N_STAGE'.

    • ARID4A|5926 ,  RCOR3|55758 ,  ACSS1|84532 ,  FAM117A|81558 ,  RARS|5917 ,  ...

  • 4 genes correlated to 'GENDER'.

    • HDHD1A|8226 ,  NCRNA00183|554203 ,  CYORF15A|246126 ,  CYORF15B|84663

  • 6 genes correlated to 'RADIATION_THERAPY'.

    • FATE1|89885 ,  TRIM5|85363 ,  LYPD3|27076 ,  TAPT1|202018 ,  RNF19B|127544 ,  ...

  • 30 genes correlated to 'KARNOFSKY_PERFORMANCE_SCORE'.

    • MT1X|4501 ,  DDX42|11325 ,  KIAA1109|84162 ,  H1FX|8971 ,  UBR4|23352 ,  ...

  • 30 genes correlated to 'HISTOLOGICAL_TYPE'.

    • KCNQ1|3784 ,  ATAD5|79915 ,  CCNF|899 ,  BIRC5|332 ,  MECOM|2122 ,  ...

  • 30 genes correlated to 'NUMBER_PACK_YEARS_SMOKED'.

    • C5ORF33|133686 ,  DSN1|79980 ,  AZU1|566 ,  C17ORF42|79736 ,  ABCA3|21 ,  ...

  • 30 genes correlated to 'YEAR_OF_TOBACCO_SMOKING_ONSET'.

    • ANKRD33|341405 ,  GPR15|2838 ,  HIST1H2BG|8339 ,  HIST1H2BJ|8970 ,  ZNF695|57116 ,  ...

  • 1 gene correlated to 'RESIDUAL_TUMOR'.

    • KATNAL2|83473

  • 30 genes correlated to 'RACE'.

    • CRYBB2|1415 ,  ULK4|54986 ,  NOTCH2NL|388677 ,  POLR2J3|548644 ,  POLR2J4|84820 ,  ...

  • No genes correlated to 'PATHOLOGY_M_STAGE', 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=30   N=NA   N=NA
YEARS_TO_BIRTH Spearman correlation test N=30 older N=11 younger N=19
PATHOLOGIC_STAGE Kruskal-Wallis test N=30        
PATHOLOGY_T_STAGE Spearman correlation test N=30 higher stage N=0 lower stage N=30
PATHOLOGY_N_STAGE Spearman correlation test N=30 higher stage N=9 lower stage N=21
PATHOLOGY_M_STAGE Wilcoxon test   N=0        
GENDER Wilcoxon test N=4 male N=4 female N=0
RADIATION_THERAPY Wilcoxon test N=6 yes N=6 no N=0
KARNOFSKY_PERFORMANCE_SCORE Spearman correlation test N=30 higher score N=22 lower score N=8
HISTOLOGICAL_TYPE Kruskal-Wallis test N=30        
NUMBER_PACK_YEARS_SMOKED Spearman correlation test N=30 higher number_pack_years_smoked N=21 lower number_pack_years_smoked N=9
YEAR_OF_TOBACCO_SMOKING_ONSET Spearman correlation test N=30 higher year_of_tobacco_smoking_onset N=20 lower year_of_tobacco_smoking_onset N=10
RESIDUAL_TUMOR Kruskal-Wallis test N=1        
RACE Kruskal-Wallis test N=30        
ETHNICITY Wilcoxon test   N=0        
Clinical variable #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

30 genes 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) 0-238.3 (median=21.6)
  censored N = 327
  death N = 187
     
  Significant markers N = 30
  associated with shorter survival NA
  associated with longer survival NA
List of top 10 genes differentially expressed by 'DAYS_TO_DEATH_OR_LAST_FUP'

Table S2.  Get Full Table List of top 10 genes significantly associated with 'Time to Death' by Cox regression test. For the survival curves, it compared quantile intervals at c(0, 0.25, 0.50, 0.75, 1) and did not try survival analysis if there is only one interval.

logrank_P Q C_index
IRX5|10265 5.27e-08 0.00037 0.381
MYO1E|4643 5.77e-08 0.00037 0.587
DKK1|22943 6.14e-08 0.00037 0.663
FAM83B|222584 1.48e-07 0.00068 0.607
GNMT|27232 4.58e-07 0.0014 0.385
FAM117A|81558 4.7e-07 0.0014 0.37
PLCD3|113026 7.17e-07 0.0019 0.612
ANAPC4|29945 8.17e-07 0.0019 0.431
PLEKHB1|58473 1.49e-06 0.003 0.38
GALNT2|2590 1.8e-06 0.0033 0.607
Clinical variable #2: 'YEARS_TO_BIRTH'

30 genes related to 'YEARS_TO_BIRTH'.

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

YEARS_TO_BIRTH Mean (SD) 65.27 (9.9)
  Significant markers N = 30
  pos. correlated 11
  neg. correlated 19
List of top 10 genes differentially expressed by 'YEARS_TO_BIRTH'

Table S4.  Get Full Table List of top 10 genes significantly correlated to 'YEARS_TO_BIRTH' by Spearman correlation test

SpearmanCorr corrP Q
GPR15|2838 -0.2631 1.358e-08 0.000147
SLC40A1|30061 0.2519 1.94e-08 0.000147
C9ORF140|89958 -0.2502 2.414e-08 0.000147
C7ORF68|29923 -0.2467 3.806e-08 0.000174
EDA2R|60401 0.2436 5.942e-08 0.000215
PLA1A|51365 0.2404 8.608e-08 0.000215
FRZB|2487 0.2402 8.846e-08 0.000215
AHRR|57491 -0.2399 9.41e-08 0.000215
SRM|6723 -0.2381 1.148e-07 0.000217
ZNF598|90850 -0.2371 1.303e-07 0.000217
Clinical variable #3: 'PATHOLOGIC_STAGE'

30 genes related to 'PATHOLOGIC_STAGE'.

Table S5.  Basic characteristics of clinical feature: 'PATHOLOGIC_STAGE'

PATHOLOGIC_STAGE Labels N
  STAGE I 5
  STAGE IA 131
  STAGE IB 139
  STAGE II 1
  STAGE IIA 50
  STAGE IIB 71
  STAGE IIIA 73
  STAGE IIIB 11
  STAGE IV 26
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'PATHOLOGIC_STAGE'

Table S6.  Get Full Table List of top 10 genes differentially expressed by 'PATHOLOGIC_STAGE'

kruskal_wallis_P Q
RASGRP2|10235 4.82e-09 8.83e-05
PTGDS|5730 2.119e-08 0.000185
FAM117A|81558 5.705e-08 0.000185
BLK|640 7.278e-08 0.000185
FAM125B|89853 7.788e-08 0.000185
RBP5|83758 8.099e-08 0.000185
SEPT1|1731 8.208e-08 0.000185
STAP1|26228 9.233e-08 0.000185
C9ORF45|81571 9.812e-08 0.000185
CCL19|6363 1.011e-07 0.000185
Clinical variable #4: 'PATHOLOGY_T_STAGE'

30 genes related to 'PATHOLOGY_T_STAGE'.

Table S7.  Basic characteristics of clinical feature: 'PATHOLOGY_T_STAGE'

PATHOLOGY_T_STAGE Mean (SD) 1.84 (0.74)
  N
  T1 169
  T2 277
  T3 47
  T4 19
     
  Significant markers N = 30
  pos. correlated 0
  neg. correlated 30
List of top 10 genes differentially expressed by 'PATHOLOGY_T_STAGE'

Table S8.  Get Full Table List of top 10 genes significantly correlated to 'PATHOLOGY_T_STAGE' by Spearman correlation test

SpearmanCorr corrP Q
FAM125B|89853 -0.2911 1.859e-11 9.88e-08
C14ORF139|79686 -0.2905 2.063e-11 9.88e-08
RASGRP2|10235 -0.2902 2.156e-11 9.88e-08
GP1BA|2811 -0.2932 2.156e-11 9.88e-08
PTGDS|5730 -0.2888 2.711e-11 9.93e-08
C9ORF45|81571 -0.2846 5.414e-11 1.65e-07
TNFRSF13B|23495 -0.2742 3.685e-10 9.64e-07
MAP4K1|11184 -0.2694 5.775e-10 1.28e-06
MS4A1|931 -0.2691 6.284e-10 1.28e-06
LOC283663|283663 -0.267 8.308e-10 1.46e-06
Clinical variable #5: 'PATHOLOGY_N_STAGE'

30 genes related to 'PATHOLOGY_N_STAGE'.

Table S9.  Basic characteristics of clinical feature: 'PATHOLOGY_N_STAGE'

PATHOLOGY_N_STAGE Mean (SD) 0.5 (0.75)
  N
  N0 331
  N1 96
  N2 74
  N3 2
     
  Significant markers N = 30
  pos. correlated 9
  neg. correlated 21
List of top 10 genes differentially expressed by 'PATHOLOGY_N_STAGE'

Table S10.  Get Full Table List of top 10 genes significantly correlated to 'PATHOLOGY_N_STAGE' by Spearman correlation test

SpearmanCorr corrP Q
ARID4A|5926 -0.2414 4.227e-08 0.000467
RCOR3|55758 -0.2399 5.103e-08 0.000467
ACSS1|84532 -0.2285 2.219e-07 0.00131
FAM117A|81558 -0.2237 4.001e-07 0.00131
RARS|5917 0.2207 5.762e-07 0.00131
FLJ42875|440556 -0.2218 6.568e-07 0.00131
EPM2AIP1|9852 -0.218 7.928e-07 0.00131
PPM1G|5496 0.2172 8.731e-07 0.00131
RRM2|6241 0.217 8.972e-07 0.00131
MRPS12|6183 0.2167 9.249e-07 0.00131
Clinical variable #6: 'PATHOLOGY_M_STAGE'

No gene related to 'PATHOLOGY_M_STAGE'.

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

PATHOLOGY_M_STAGE Labels N
  class0 346
  class1 25
     
  Significant markers N = 0
Clinical variable #7: 'GENDER'

4 genes related to 'GENDER'.

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

GENDER Labels N
  FEMALE 277
  MALE 238
     
  Significant markers N = 4
  Higher in MALE 4
  Higher in FEMALE 0
List of 4 genes differentially expressed by 'GENDER'

Table S13.  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
HDHD1A|8226 15917 7.306e-24 9.56e-21 0.7575
NCRNA00183|554203 16568 2.092e-22 2.39e-19 0.7487
CYORF15A|246126 8493 2.149e-21 2.32e-18 0.9912
CYORF15B|84663 8267 5.228e-21 5.32e-18 0.9924
Clinical variable #8: 'RADIATION_THERAPY'

6 genes related to 'RADIATION_THERAPY'.

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

RADIATION_THERAPY Labels N
  NO 408
  YES 61
     
  Significant markers N = 6
  Higher in YES 6
  Higher in NO 0
List of 6 genes differentially expressed by 'RADIATION_THERAPY'

Table S15.  Get Full Table List of 6 genes differentially expressed by 'RADIATION_THERAPY'

W(pos if higher in 'YES') wilcoxontestP Q AUC
FATE1|89885 15254 3.703e-06 0.0382 0.6885
TRIM5|85363 7911 4.416e-06 0.0382 0.6821
LYPD3|27076 16877 7.14e-06 0.0382 0.6781
TAPT1|202018 8044 8.348e-06 0.0382 0.6768
RNF19B|127544 8434 4.886e-05 0.179 0.6611
HIST1H2AL|8332 9778.5 8.207e-05 0.251 0.6744
Clinical variable #9: 'KARNOFSKY_PERFORMANCE_SCORE'

30 genes related to 'KARNOFSKY_PERFORMANCE_SCORE'.

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

KARNOFSKY_PERFORMANCE_SCORE Mean (SD) 78.37 (29)
  Significant markers N = 30
  pos. correlated 22
  neg. correlated 8
List of top 10 genes differentially expressed by 'KARNOFSKY_PERFORMANCE_SCORE'

Table S17.  Get Full Table List of top 10 genes significantly correlated to 'KARNOFSKY_PERFORMANCE_SCORE' by Spearman correlation test

SpearmanCorr corrP Q
MT1X|4501 -0.4145 5.781e-07 0.0106
DDX42|11325 0.4043 1.158e-06 0.0106
KIAA1109|84162 0.386 3.768e-06 0.0166
H1FX|8971 -0.3813 5.057e-06 0.0166
UBR4|23352 0.3806 5.266e-06 0.0166
RPL36|25873 -0.3801 5.446e-06 0.0166
SUPT6H|6830 0.3725 8.639e-06 0.0226
BIRC6|57448 0.3673 1.172e-05 0.0268
SPAG9|9043 0.3544 2.475e-05 0.0438
ZNF627|199692 -0.3535 2.6e-05 0.0438
Clinical variable #10: 'HISTOLOGICAL_TYPE'

30 genes related to 'HISTOLOGICAL_TYPE'.

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

HISTOLOGICAL_TYPE Labels N
  LUNG ACINAR ADENOCARCINOMA 18
  LUNG ADENOCARCINOMA MIXED SUBTYPE 107
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) 320
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS 5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS 19
  LUNG CLEAR CELL ADENOCARCINOMA 2
  LUNG MICROPAPILLARY ADENOCARCINOMA 3
  LUNG MUCINOUS ADENOCARCINOMA 2
  LUNG PAPILLARY ADENOCARCINOMA 23
  LUNG SIGNET RING ADENOCARCINOMA 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA 5
  MUCINOUS (COLLOID) CARCINOMA 10
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'HISTOLOGICAL_TYPE'

Table S19.  Get Full Table List of top 10 genes differentially expressed by 'HISTOLOGICAL_TYPE'

kruskal_wallis_P Q
KCNQ1|3784 2.448e-09 4.49e-05
ATAD5|79915 7.057e-08 0.000623
CCNF|899 1.435e-07 0.000623
BIRC5|332 2.454e-07 0.000623
MECOM|2122 2.558e-07 0.000623
GINS2|51659 2.722e-07 0.000623
EPR1|8475 2.823e-07 0.000623
CCNE2|9134 3.085e-07 0.000623
KPNA2|3838 3.479e-07 0.000623
SLC44A4|80736 3.574e-07 0.000623
Clinical variable #11: 'NUMBER_PACK_YEARS_SMOKED'

30 genes related to 'NUMBER_PACK_YEARS_SMOKED'.

Table S20.  Basic characteristics of clinical feature: 'NUMBER_PACK_YEARS_SMOKED'

NUMBER_PACK_YEARS_SMOKED Mean (SD) 41.81 (27)
  Significant markers N = 30
  pos. correlated 21
  neg. correlated 9
List of top 10 genes differentially expressed by 'NUMBER_PACK_YEARS_SMOKED'

Table S21.  Get Full Table List of top 10 genes significantly correlated to 'NUMBER_PACK_YEARS_SMOKED' by Spearman correlation test

SpearmanCorr corrP Q
C5ORF33|133686 0.2523 1.748e-06 0.032
DSN1|79980 0.23 1.382e-05 0.09
AZU1|566 -0.2489 1.473e-05 0.09
C17ORF42|79736 0.2219 2.794e-05 0.0914
ABCA3|21 -0.2192 3.525e-05 0.0914
C18ORF19|125228 0.2187 3.665e-05 0.0914
SYCE2|256126 0.2195 3.919e-05 0.0914
FANCB|2187 0.2165 4.428e-05 0.0914
ETS2|2114 -0.214 5.417e-05 0.0914
C3ORF26|84319 0.2128 5.997e-05 0.0914
Clinical variable #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

30 genes related to 'YEAR_OF_TOBACCO_SMOKING_ONSET'.

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

YEAR_OF_TOBACCO_SMOKING_ONSET Mean (SD) 1964.97 (12)
  Significant markers N = 30
  pos. correlated 20
  neg. correlated 10
List of top 10 genes differentially expressed by 'YEAR_OF_TOBACCO_SMOKING_ONSET'

Table S23.  Get Full Table List of top 10 genes significantly correlated to 'YEAR_OF_TOBACCO_SMOKING_ONSET' by Spearman correlation test

SpearmanCorr corrP Q
ANKRD33|341405 0.387 7.375e-08 0.00135
GPR15|2838 0.3084 4.33e-07 0.00397
HIST1H2BG|8339 0.3002 7.059e-07 0.0043
HIST1H2BJ|8970 0.2911 9.397e-07 0.0043
ZNF695|57116 0.2796 3.185e-06 0.0117
HIST1H4E|8367 0.3062 3.9e-06 0.0119
JMJD6|23210 0.2711 5.294e-06 0.0129
SLC7A5|8140 0.2704 5.618e-06 0.0129
FOLR1|2348 -0.2678 7.221e-06 0.0136
C7ORF51|222950 0.2694 7.438e-06 0.0136
Clinical variable #13: 'RESIDUAL_TUMOR'

One gene related to 'RESIDUAL_TUMOR'.

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

RESIDUAL_TUMOR Labels N
  R0 344
  R1 13
  R2 4
  RX 25
     
  Significant markers N = 1
List of one gene differentially expressed by 'RESIDUAL_TUMOR'

Table S25.  Get Full Table List of one gene differentially expressed by 'RESIDUAL_TUMOR'

kruskal_wallis_P Q
KATNAL2|83473 1.571e-05 0.288
Clinical variable #14: 'RACE'

30 genes related to 'RACE'.

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

RACE Labels N
  AMERICAN INDIAN OR ALASKA NATIVE 1
  ASIAN 8
  BLACK OR AFRICAN AMERICAN 52
  WHITE 388
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'RACE'

Table S27.  Get Full Table List of top 10 genes differentially expressed by 'RACE'

kruskal_wallis_P Q
CRYBB2|1415 6.67e-11 1.22e-06
ULK4|54986 3.389e-09 3.1e-05
NOTCH2NL|388677 9.379e-09 5.73e-05
POLR2J3|548644 4.453e-08 0.000204
POLR2J4|84820 4.67e-07 0.00171
TUBB8|347688 6.631e-07 0.00202
SPDYE2|441273 1.273e-06 0.00333
LOC90784|90784 1.525e-06 0.00349
PRSS45|377047 1.843e-06 0.00375
LOC202781|202781 3.096e-06 0.00554
Clinical variable #15: 'ETHNICITY'

No gene related to 'ETHNICITY'.

Table S28.  Basic characteristics of clinical feature: 'ETHNICITY'

ETHNICITY Labels N
  HISPANIC OR LATINO 7
  NOT HISPANIC OR LATINO 383
     
  Significant markers N = 0
Methods & Data
Input

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

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

  • Number of patients = 515

  • Number of genes = 18319

  • 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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