Correlation between mRNAseq expression and clinical features
Skin Cutaneous Melanoma (Metastatic)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1TM79KQ
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/C1TM79KQ
Overview
Introduction

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

Summary

Testing the association between 18059 genes and 14 clinical features across 368 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 'TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP'.

    • GATAD2A|54815 ,  GCNT1|2650 ,  NMI|9111 ,  PEPD|5184 ,  DPM1|8813 ,  ...

  • 30 genes correlated to 'DAYS_TO_DEATH_OR_LAST_FUP'.

    • GATAD2A|54815 ,  APOBEC3G|60489 ,  CCL8|6355 ,  GBP2|2634 ,  UBA7|7318 ,  ...

  • 30 genes correlated to 'YEARS_TO_BIRTH'.

    • CMBL|134147 ,  ACOX2|8309 ,  MGST2|4258 ,  NMNAT3|349565 ,  LOXL4|84171 ,  ...

  • 3 genes correlated to 'PATHOLOGIC_STAGE'.

    • RAI14|26064 ,  SEMA3E|9723 ,  DIS3L2|129563

  • 30 genes correlated to 'PATHOLOGY_T_STAGE'.

    • INHA|3623 ,  POU5F1B|5462 ,  KYNU|8942 ,  GSDMD|79792 ,  TNFSF13B|10673 ,  ...

  • 30 genes correlated to 'PATHOLOGY_N_STAGE'.

    • C12ORF62|84987 ,  PTPRG|5793 ,  IL17RD|54756 ,  HIST1H1C|3006 ,  MAML3|55534 ,  ...

  • 2 genes correlated to 'MELANOMA_PRIMARY_KNOWN'.

    • ST6GALNAC3|256435 ,  ICOSLG|23308

  • 30 genes correlated to 'BRESLOW_THICKNESS'.

    • C6ORF218|221718 ,  ATP6V0A1|535 ,  SLC7A8|23428 ,  LOC100240735|100240735 ,  TNFSF13B|10673 ,  ...

  • 5 genes correlated to 'GENDER'.

    • CYORF15A|246126 ,  HDHD1A|8226 ,  CYORF15B|84663 ,  NCRNA00183|554203 ,  CA5BP|340591

  • No genes correlated to 'PATHOLOGY_M_STAGE', 'MELANOMA_ULCERATION', 'RADIATION_THERAPY', 'RACE', 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
TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP Cox regression test N=30   N=NA   N=NA
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=3 younger N=27
PATHOLOGIC_STAGE Kruskal-Wallis test N=3        
PATHOLOGY_T_STAGE Spearman correlation test N=30 higher stage N=4 lower stage N=26
PATHOLOGY_N_STAGE Spearman correlation test N=30 higher stage N=12 lower stage N=18
PATHOLOGY_M_STAGE Wilcoxon test   N=0        
MELANOMA_ULCERATION Wilcoxon test   N=0        
MELANOMA_PRIMARY_KNOWN Wilcoxon test N=2 yes N=2 no N=0
BRESLOW_THICKNESS Spearman correlation test N=30 higher breslow_thickness N=10 lower breslow_thickness N=20
GENDER Wilcoxon test N=5 male N=5 female N=0
RADIATION_THERAPY Wilcoxon test   N=0        
RACE Kruskal-Wallis test   N=0        
ETHNICITY Wilcoxon test   N=0        
Clinical variable #1: 'TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP'

30 genes related to 'TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP'.

Table S1.  Basic characteristics of clinical feature: 'TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP'

TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP Duration (Months) 0-346.5 (median=46)
  censored N = 128
  death N = 125
     
  Significant markers N = 30
  associated with shorter survival NA
  associated with longer survival NA
List of top 10 genes differentially expressed by 'TIME_FROM_SPECIMEN_DX_TO_DEATH_OR_LAST_FUP'

Table S2.  Get Full Table List of top 10 genes significantly associated with 'Time from Specimen Diagnosis 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
GATAD2A|54815 6.13e-08 0.00099 0.626
GCNT1|2650 1.85e-07 0.00099 0.368
NMI|9111 1.91e-07 0.00099 0.345
PEPD|5184 2.69e-07 0.00099 0.569
DPM1|8813 2.82e-07 0.00099 0.425
TLR2|7097 3.29e-07 0.00099 0.392
DENND3|22898 5e-07 0.0013 0.4
KIT|3815 6.62e-07 0.0015 0.643
CLEC7A|64581 7.74e-07 0.0015 0.377
SP8|221833 8.06e-07 0.0015 0.592
Clinical variable #2: 'DAYS_TO_DEATH_OR_LAST_FUP'

30 genes related to 'DAYS_TO_DEATH_OR_LAST_FUP'.

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

DAYS_TO_DEATH_OR_LAST_FUP Duration (Months) 0.2-369.9 (median=52.3)
  censored N = 173
  death N = 194
     
  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 S4.  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
GATAD2A|54815 2.05e-10 3.7e-06 0.614
APOBEC3G|60489 1.13e-09 1e-05 0.374
CCL8|6355 1.54e-08 8e-05 0.375
GBP2|2634 1.77e-08 8e-05 0.354
UBA7|7318 3.81e-08 0.00014 0.355
GBP4|115361 8.51e-08 0.00021 0.36
TLR2|7097 9.03e-08 0.00021 0.395
SAMD9L|219285 9.22e-08 0.00021 0.363
NMI|9111 1.25e-07 0.00025 0.358
STAT4|6775 1.55e-07 0.00026 0.381
Clinical variable #3: 'YEARS_TO_BIRTH'

30 genes related to 'YEARS_TO_BIRTH'.

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

YEARS_TO_BIRTH Mean (SD) 56.32 (16)
  Significant markers N = 30
  pos. correlated 3
  neg. correlated 27
List of top 10 genes differentially expressed by 'YEARS_TO_BIRTH'

Table S6.  Get Full Table List of top 10 genes significantly correlated to 'YEARS_TO_BIRTH' by Spearman correlation test

SpearmanCorr corrP Q
CMBL|134147 -0.3188 5.979e-10 1.08e-05
ACOX2|8309 -0.3037 4.287e-09 3.87e-05
MGST2|4258 -0.2909 1.894e-08 0.000114
NMNAT3|349565 -0.2725 1.571e-07 0.000709
LOXL4|84171 -0.2663 2.921e-07 0.000969
MAOB|4129 -0.2654 3.221e-07 0.000969
OR2A9P|441295 -0.2603 5.514e-07 0.00142
PRDX6|9588 -0.257 7.738e-07 0.00175
MOSC1|64757 -0.2554 9.072e-07 0.00178
FAM84B|157638 -0.2546 9.834e-07 0.00178
Clinical variable #4: 'PATHOLOGIC_STAGE'

3 genes related to 'PATHOLOGIC_STAGE'.

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

PATHOLOGIC_STAGE Labels N
  I/II NOS 13
  STAGE 0 7
  STAGE I 29
  STAGE IA 18
  STAGE IB 28
  STAGE II 26
  STAGE IIA 14
  STAGE IIB 19
  STAGE IIC 15
  STAGE III 39
  STAGE IIIA 15
  STAGE IIIB 35
  STAGE IIIC 55
  STAGE IV 21
     
  Significant markers N = 3
List of 3 genes differentially expressed by 'PATHOLOGIC_STAGE'

Table S8.  Get Full Table List of 3 genes differentially expressed by 'PATHOLOGIC_STAGE'

kruskal_wallis_P Q
RAI14|26064 1.294e-05 0.211
SEMA3E|9723 2.341e-05 0.211
DIS3L2|129563 3.696e-05 0.222
Clinical variable #5: 'PATHOLOGY_T_STAGE'

30 genes related to 'PATHOLOGY_T_STAGE'.

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

PATHOLOGY_T_STAGE Mean (SD) 2.45 (1.2)
  N
  T0 23
  T1 41
  T2 73
  T3 81
  T4 68
     
  Significant markers N = 30
  pos. correlated 4
  neg. correlated 26
List of top 10 genes differentially expressed by 'PATHOLOGY_T_STAGE'

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

SpearmanCorr corrP Q
INHA|3623 -0.2827 1.399e-06 0.0224
POU5F1B|5462 -0.2784 3.242e-06 0.0224
KYNU|8942 -0.2697 3.721e-06 0.0224
GSDMD|79792 -0.2639 6.067e-06 0.0274
TNFSF13B|10673 -0.2581 1.022e-05 0.0369
MUL1|79594 0.2538 1.393e-05 0.0377
LOC148709|148709 0.2581 1.46e-05 0.0377
LOC100240735|100240735 -0.2591 1.869e-05 0.0402
FGL2|10875 -0.249 2.041e-05 0.0402
LILRB1|10859 -0.2453 2.82e-05 0.0402
Clinical variable #6: 'PATHOLOGY_N_STAGE'

30 genes related to 'PATHOLOGY_N_STAGE'.

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

PATHOLOGY_N_STAGE Mean (SD) 0.85 (1.1)
  N
  N0 177
  N1 66
  N2 39
  N3 45
     
  Significant markers N = 30
  pos. correlated 12
  neg. correlated 18
List of top 10 genes differentially expressed by 'PATHOLOGY_N_STAGE'

Table S12.  Get Full Table List of top 10 genes significantly correlated to 'PATHOLOGY_N_STAGE' by Spearman correlation test

SpearmanCorr corrP Q
C12ORF62|84987 0.2587 2.118e-06 0.0383
PTPRG|5793 -0.2367 1.527e-05 0.112
IL17RD|54756 -0.2314 2.377e-05 0.112
HIST1H1C|3006 0.2289 2.919e-05 0.112
MAML3|55534 -0.2282 3.102e-05 0.112
RNF168|165918 -0.2242 4.292e-05 0.129
CHCHD10|400916 0.2152 8.733e-05 0.196
RAI14|26064 -0.2149 8.992e-05 0.196
DLC1|10395 -0.2118 0.0001137 0.196
MAP2|4133 -0.211 0.0001207 0.196
Clinical variable #7: 'PATHOLOGY_M_STAGE'

No gene related to 'PATHOLOGY_M_STAGE'.

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

PATHOLOGY_M_STAGE Labels N
  class0 320
  class1 22
     
  Significant markers N = 0
Clinical variable #8: 'MELANOMA_ULCERATION'

No gene related to 'MELANOMA_ULCERATION'.

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

MELANOMA_ULCERATION Labels N
  NO 134
  YES 91
     
  Significant markers N = 0
Clinical variable #9: 'MELANOMA_PRIMARY_KNOWN'

2 genes related to 'MELANOMA_PRIMARY_KNOWN'.

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

MELANOMA_PRIMARY_KNOWN Labels N
  NO 47
  YES 321
     
  Significant markers N = 2
  Higher in YES 2
  Higher in NO 0
List of 2 genes differentially expressed by 'MELANOMA_PRIMARY_KNOWN'

Table S16.  Get Full Table List of 2 genes differentially expressed by 'MELANOMA_PRIMARY_KNOWN'

W(pos if higher in 'YES') wilcoxontestP Q AUC
ST6GALNAC3|256435 10510 1.333e-05 0.241 0.6966
ICOSLG|23308 4715.5 3.307e-05 0.299 0.6874
Clinical variable #10: 'BRESLOW_THICKNESS'

30 genes related to 'BRESLOW_THICKNESS'.

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

BRESLOW_THICKNESS Mean (SD) 3.47 (4.7)
  Significant markers N = 30
  pos. correlated 10
  neg. correlated 20
List of top 10 genes differentially expressed by 'BRESLOW_THICKNESS'

Table S18.  Get Full Table List of top 10 genes significantly correlated to 'BRESLOW_THICKNESS' by Spearman correlation test

SpearmanCorr corrP Q
C6ORF218|221718 0.304 4.548e-07 0.00465
ATP6V0A1|535 0.2964 8.176e-07 0.00465
SLC7A8|23428 0.2962 8.306e-07 0.00465
LOC100240735|100240735 -0.3038 1.03e-06 0.00465
TNFSF13B|10673 -0.2902 1.475e-06 0.00511
CRTAP|10491 0.2879 1.713e-06 0.00511
FCRL6|343413 -0.2887 2.005e-06 0.00511
PTMA|5757 -0.2847 2.264e-06 0.00511
RGS18|64407 -0.2837 3.35e-06 0.00584
ASF1A|25842 -0.2796 3.476e-06 0.00584
Clinical variable #11: 'GENDER'

5 genes related to 'GENDER'.

Table S19.  Basic characteristics of clinical feature: 'GENDER'

GENDER Labels N
  FEMALE 138
  MALE 230
     
  Significant markers N = 5
  Higher in MALE 5
  Higher in FEMALE 0
List of 5 genes differentially expressed by 'GENDER'

Table S20.  Get Full Table List of 5 genes differentially expressed by 'GENDER'. 25 significant gene(s) located in sex chromosomes is(are) filtered out.

W(pos if higher in 'MALE') wilcoxontestP Q AUC
CYORF15A|246126 6432 7.054e-18 9.1e-15 0.9988
HDHD1A|8226 8638 2.482e-13 2.8e-10 0.7279
CYORF15B|84663 4124 2.448e-12 2.46e-09 0.9961
NCRNA00183|554203 9326 3.509e-11 3.17e-08 0.7062
CA5BP|340591 10468 4.564e-08 3.05e-05 0.6702
Clinical variable #12: 'RADIATION_THERAPY'

No gene related to 'RADIATION_THERAPY'.

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

RADIATION_THERAPY Labels N
  NO 319
  YES 48
     
  Significant markers N = 0
Clinical variable #13: 'RACE'

No gene related to 'RACE'.

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

RACE Labels N
  ASIAN 5
  BLACK OR AFRICAN AMERICAN 1
  WHITE 354
     
  Significant markers N = 0
Clinical variable #14: 'ETHNICITY'

No gene related to 'ETHNICITY'.

Table S23.  Basic characteristics of clinical feature: 'ETHNICITY'

ETHNICITY Labels N
  HISPANIC OR LATINO 7
  NOT HISPANIC OR LATINO 353
     
  Significant markers N = 0
Methods & Data
Input

  • Expresson data file = SKCM-TM.uncv2.mRNAseq_RSEM_normalized_log2.txt

  • Clinical data file = SKCM-TM.merged_data.txt

  • Number of patients = 368

  • Number of genes = 18059

  • Number of clinical features = 14

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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