Correlation between mRNAseq expression and clinical features
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 18296 genes and 12 clinical features across 1076 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 11 clinical features related to at least one genes.

  • 30 genes correlated to 'DAYS_TO_DEATH_OR_LAST_FUP'.

    • PGK1|5230 ,  NFKBIA|4792 ,  TNFRSF14|8764 ,  LRP11|84918 ,  CEL|1056 ,  ...

  • 30 genes correlated to 'YEARS_TO_BIRTH'.

    • ESR1|2099 ,  DSC2|1824 ,  TMEFF1|8577 ,  ZNF521|25925 ,  LRFN5|145581 ,  ...

  • 30 genes correlated to 'NEOPLASM_DISEASESTAGE'.

    • MMRN1|22915 ,  SVEP1|79987 ,  ABCA9|10350 ,  C18ORF34|374864 ,  C16ORF89|146556 ,  ...

  • 30 genes correlated to 'PATHOLOGY_T_STAGE'.

    • ZMYM6|9204 ,  NDNL2|56160 ,  ERMN|57471 ,  IKZF4|64375 ,  ARAF|369 ,  ...

  • 30 genes correlated to 'PATHOLOGY_N_STAGE'.

    • HMSD|284293 ,  SVEP1|79987 ,  HTR2B|3357 ,  NR2F2|7026 ,  F2R|2149 ,  ...

  • 1 gene correlated to 'PATHOLOGY_M_STAGE'.

    • RBM25|58517

  • 24 genes correlated to 'GENDER'.

    • SLC39A11|201266 ,  FAM104A|84923 ,  CSNK1D|1453 ,  GINS2|51659 ,  TMEM49|81671 ,  ...

  • 30 genes correlated to 'HISTOLOGICAL_TYPE'.

    • CDH1|999 ,  RAPGEF3|10411 ,  TENC1|23371 ,  AVPR2|554 ,  PSMD12|5718 ,  ...

  • 30 genes correlated to 'RADIATIONS_RADIATION_REGIMENINDICATION'.

    • SELO|83642 ,  CAPN10|11132 ,  ZBTB17|7709 ,  RING1|6015 ,  CROCC|9696 ,  ...

  • 30 genes correlated to 'NUMBER_OF_LYMPH_NODES'.

    • HMSD|284293 ,  SNED1|25992 ,  PODN|127435 ,  POU4F1|5457 ,  CD1A|909 ,  ...

  • 30 genes correlated to 'RACE'.

    • CRYBB2|1415 ,  CROCCL1|84809 ,  FAM3A|60343 ,  LRRC37A2|474170 ,  C14ORF167|55449 ,  ...

  • No genes correlated to '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 shorter survival N=12 longer survival N=18
YEARS_TO_BIRTH Spearman correlation test N=30 older N=1 younger N=29
NEOPLASM_DISEASESTAGE Kruskal-Wallis test N=30        
PATHOLOGY_T_STAGE Spearman correlation test N=30 higher stage N=5 lower stage N=25
PATHOLOGY_N_STAGE Spearman correlation test N=30 higher stage N=21 lower stage N=9
PATHOLOGY_M_STAGE Wilcoxon test N=1 class1 N=1 class0 N=0
GENDER Wilcoxon test N=24 male N=24 female N=0
HISTOLOGICAL_TYPE Kruskal-Wallis test N=30        
RADIATIONS_RADIATION_REGIMENINDICATION Wilcoxon test N=30 yes N=30 no N=0
NUMBER_OF_LYMPH_NODES Spearman correlation test N=30 higher number_of_lymph_nodes N=23 lower number_of_lymph_nodes N=7
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) 0-234.3 (median=24.6)
  censored N = 943
  death N = 132
     
  Significant markers N = 30
  associated with shorter survival 12
  associated with longer survival 18
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

HazardRatio Wald_P Q C_index
PGK1|5230 1.96 1.269e-07 0.0023 0.67
NFKBIA|4792 0.48 2.979e-07 0.0027 0.37
TNFRSF14|8764 0.67 2.344e-06 0.0094 0.396
LRP11|84918 1.69 2.449e-06 0.0094 0.613
CEL|1056 1.21 2.576e-06 0.0094 0.614
RAC2|5880 0.71 4.932e-06 0.015 0.4
PCMT1|5110 1.99 6.81e-06 0.017 0.643
CEBPD|1052 0.73 7.371e-06 0.017 0.412
PARP3|10039 0.65 8.493e-06 0.017 0.383
NUP43|348995 2.1 9.115e-06 0.017 0.586
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) 58.62 (13)
  Significant markers N = 30
  pos. correlated 1
  neg. correlated 29
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
ESR1|2099 0.3441 7.373e-31 1.35e-26
DSC2|1824 -0.2619 4.203e-18 3.85e-14
TMEFF1|8577 -0.2535 5.06e-17 3.09e-13
ZNF521|25925 -0.2502 1.329e-16 5.5e-13
LRFN5|145581 -0.2528 1.502e-16 5.5e-13
RELN|5649 -0.2522 2.171e-16 6.62e-13
DZIP1|22873 -0.2468 3.496e-16 8.62e-13
FAT2|2196 -0.2468 3.77e-16 8.62e-13
ASTN1|460 -0.2499 1.103e-15 2.18e-12
IGSF10|285313 -0.2427 1.191e-15 2.18e-12
Clinical variable #3: 'NEOPLASM_DISEASESTAGE'

30 genes related to 'NEOPLASM_DISEASESTAGE'.

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

NEOPLASM_DISEASESTAGE Labels N
  STAGE I 89
  STAGE IA 83
  STAGE IB 9
  STAGE II 3
  STAGE IIA 359
  STAGE IIB 248
  STAGE III 2
  STAGE IIIA 151
  STAGE IIIB 29
  STAGE IIIC 63
  STAGE IV 20
  STAGE TIS 1
  STAGE X 14
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'NEOPLASM_DISEASESTAGE'

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

kruskal_wallis_P Q
MMRN1|22915 6.202e-08 0.000745
SVEP1|79987 8.14e-08 0.000745
ABCA9|10350 1.23e-07 0.00075
C18ORF34|374864 2.065e-07 0.00087
C16ORF89|146556 2.917e-07 0.00087
GREM2|64388 3.816e-07 0.00087
GLI1|2735 4.12e-07 0.00087
IGF1|3479 4.581e-07 0.00087
ZFP36|7538 4.861e-07 0.00087
LHFP|10186 5.69e-07 0.00087
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) 1.94 (0.73)
  N
  T1 277
  T2 624
  T3 131
  T4 40
     
  Significant markers N = 30
  pos. correlated 5
  neg. correlated 25
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
ZMYM6|9204 -0.1817 2.067e-09 3.78e-05
NDNL2|56160 -0.1656 4.973e-08 0.000268
ERMN|57471 -0.1658 5.002e-08 0.000268
IKZF4|64375 -0.1644 6.137e-08 0.000268
ARAF|369 0.1635 7.327e-08 0.000268
ZBTB1|22890 -0.1603 1.306e-07 0.000341
SEMA3D|223117 -0.1607 1.318e-07 0.000341
CD1A|909 -0.1662 1.491e-07 0.000341
PTGER3|5733 -0.1574 2.234e-07 0.000401
SELE|6401 -0.1571 2.416e-07 0.000401
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) 0.77 (0.91)
  N
  N0 509
  N1 354
  N2 118
  N3 75
     
  Significant markers N = 30
  pos. correlated 21
  neg. correlated 9
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
HMSD|284293 -0.217 5.052e-08 0.00047
SVEP1|79987 0.1667 5.133e-08 0.00047
HTR2B|3357 0.1615 1.322e-07 0.000681
NR2F2|7026 0.1606 1.535e-07 0.000681
F2R|2149 0.1587 2.192e-07 0.000681
NUDT4|11163 0.1585 2.233e-07 0.000681
CXCR7|57007 0.1548 4.326e-07 0.00113
SNED1|25992 0.1529 5.924e-07 0.00135
TTC22|55001 -0.1516 9.094e-07 0.00185
CHI3L2|1117 -0.1484 1.28e-06 0.00219
Clinical variable #6: 'PATHOLOGY_M_STAGE'

One gene related to 'PATHOLOGY_M_STAGE'.

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

PATHOLOGY_M_STAGE Labels N
  class0 892
  class1 21
     
  Significant markers N = 1
  Higher in class1 1
  Higher in class0 0
List of one gene differentially expressed by 'PATHOLOGY_M_STAGE'

Table S12.  Get Full Table List of one gene differentially expressed by 'PATHOLOGY_M_STAGE'

W(pos if higher in 'class1') wilcoxontestP Q AUC
RBM25|58517 4018 7.574e-06 0.139 0.7855
Clinical variable #7: 'GENDER'

24 genes related to 'GENDER'.

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

GENDER Labels N
  FEMALE 1065
  MALE 11
     
  Significant markers N = 24
  Higher in MALE 24
  Higher in FEMALE 0
List of top 10 genes differentially expressed by 'GENDER'

Table S14.  Get Full Table List of top 10 genes differentially expressed by 'GENDER'. 6 significant gene(s) located in sex chromosomes is(are) filtered out.

W(pos if higher in 'MALE') wilcoxontestP Q AUC
SLC39A11|201266 10635 3.182e-06 0.0116 0.9078
FAM104A|84923 10569 4.341e-06 0.012 0.9022
CSNK1D|1453 10399 9.486e-06 0.0193 0.8877
GINS2|51659 10321 1.346e-05 0.0246 0.881
TMEM49|81671 10278 1.628e-05 0.0271 0.8773
ASS1|445 1518 2.321e-05 0.0325 0.8704
TAF4|6874 10176 2.541e-05 0.0325 0.8686
MSMB|4477 9506 2.574e-05 0.0325 0.8685
C15ORF52|388115 1554 2.711e-05 0.0325 0.8673
DHRS2|10202 10074 2.842e-05 0.0325 0.8664
Clinical variable #8: 'HISTOLOGICAL_TYPE'

30 genes related to 'HISTOLOGICAL_TYPE'.

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

HISTOLOGICAL_TYPE Labels N
  INFILTRATING CARCINOMA NOS 1
  INFILTRATING DUCTAL CARCINOMA 776
  INFILTRATING LOBULAR CARCINOMA 194
  MEDULLARY CARCINOMA 6
  METAPLASTIC CARCINOMA 4
  MIXED HISTOLOGY (PLEASE SPECIFY) 29
  MUCINOUS CARCINOMA 17
  OTHER SPECIFY 48
     
  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
CDH1|999 6.131e-63 1.12e-58
RAPGEF3|10411 6.662e-46 6.09e-42
TENC1|23371 1.857e-43 1.13e-39
AVPR2|554 4.953e-43 2.27e-39
PSMD12|5718 1.495e-42 5.47e-39
LTBP4|8425 2.768e-42 8.44e-39
USHBP1|83878 4.628e-41 1.21e-37
CSE1L|1434 6.485e-41 1.48e-37
PSMD14|10213 7.753e-41 1.58e-37
GMPS|8833 1.391e-40 2.54e-37
Clinical variable #9: 'RADIATIONS_RADIATION_REGIMENINDICATION'

30 genes related to 'RADIATIONS_RADIATION_REGIMENINDICATION'.

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

RADIATIONS_RADIATION_REGIMENINDICATION Labels N
  NO 290
  YES 786
     
  Significant markers N = 30
  Higher in YES 30
  Higher in NO 0
List of top 10 genes differentially expressed by 'RADIATIONS_RADIATION_REGIMENINDICATION'

Table S18.  Get Full Table List of top 10 genes differentially expressed by 'RADIATIONS_RADIATION_REGIMENINDICATION'

W(pos if higher in 'YES') wilcoxontestP Q AUC
SELO|83642 152293 2.396e-17 4.38e-13 0.6681
CAPN10|11132 150332 9.041e-16 7.21e-12 0.6595
ZBTB17|7709 150183 1.182e-15 7.21e-12 0.6589
RING1|6015 149719 2.707e-15 1.24e-11 0.6568
CROCC|9696 149191 6.864e-15 2.41e-11 0.6545
ZNF513|130557 149110 7.908e-15 2.41e-11 0.6542
PAK2|5062 79502 2.527e-14 6.61e-11 0.6512
C19ORF6|91304 147891 6.404e-14 1.46e-10 0.6488
MIB2|142678 147656 9.506e-14 1.74e-10 0.6478
ANAPC2|29882 147639 9.781e-14 1.74e-10 0.6477
Clinical variable #10: 'NUMBER_OF_LYMPH_NODES'

30 genes related to 'NUMBER_OF_LYMPH_NODES'.

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

NUMBER_OF_LYMPH_NODES Mean (SD) 2.36 (4.6)
  Significant markers N = 30
  pos. correlated 23
  neg. correlated 7
List of top 10 genes differentially expressed by 'NUMBER_OF_LYMPH_NODES'

Table S20.  Get Full Table List of top 10 genes significantly correlated to 'NUMBER_OF_LYMPH_NODES' by Spearman correlation test

SpearmanCorr corrP Q
HMSD|284293 -0.2373 2.522e-08 0.000461
SNED1|25992 0.1757 9.758e-08 0.000566
PODN|127435 0.175 1.104e-07 0.000566
POU4F1|5457 -0.2313 1.237e-07 0.000566
CD1A|909 -0.1704 6.282e-07 0.0023
NUDT4|11163 0.1629 7.953e-07 0.00235
HTR2B|3357 0.1616 9.714e-07 0.00235
CERCAM|51148 0.1612 1.028e-06 0.00235
CBFA2T3|863 0.1584 1.589e-06 0.00323
F2R|2149 0.1566 2.089e-06 0.00366
Clinical variable #11: 'RACE'

30 genes related to 'RACE'.

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

RACE Labels N
  AMERICAN INDIAN OR ALASKA NATIVE 1
  ASIAN 61
  BLACK OR AFRICAN AMERICAN 172
  WHITE 745
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'RACE'

Table S22.  Get Full Table List of top 10 genes differentially expressed by 'RACE'

kruskal_wallis_P Q
CRYBB2|1415 1.933e-34 3.54e-30
CROCCL1|84809 1.544e-33 1.41e-29
FAM3A|60343 6.961e-33 4.25e-29
LRRC37A2|474170 3.87e-30 1.77e-26
C14ORF167|55449 1.626e-29 5.95e-26
LOC90784|90784 1.702e-28 5.19e-25
TRMT2A|27037 8.187e-28 2.14e-24
TRABD|80305 9.952e-28 2.28e-24
TOP1MT|116447 1.166e-27 2.37e-24
TSPO|706 1.462e-27 2.67e-24
Clinical variable #12: 'ETHNICITY'

No gene related to 'ETHNICITY'.

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

ETHNICITY Labels N
  HISPANIC OR LATINO 38
  NOT HISPANIC OR LATINO 864
     
  Significant markers N = 0
Methods & Data
Input

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

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

  • Number of patients = 1076

  • Number of genes = 18296

  • Number of clinical features = 12

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.

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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