Correlation between mRNAseq expression and clinical features
Liver Hepatocellular Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
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/C17080VG
Overview
Introduction

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

Summary

Testing the association between 17745 genes and 12 clinical features across 371 samples, statistically thresholded by P value < 0.05 and Q value < 0.3, 8 clinical features related to at least one genes.

  • 30 genes correlated to 'DAYS_TO_DEATH_OR_LAST_FUP'.

    • UCK2|7371 ,  SFPQ|6421 ,  CLEC3B|7123 ,  GTPBP4|23560 ,  CAD|790 ,  ...

  • 30 genes correlated to 'YEARS_TO_BIRTH'.

    • CDCA7|83879 ,  EPCAM|4072 ,  RAB3D|9545 ,  PTK7|5754 ,  OSGIN1|29948 ,  ...

  • 30 genes correlated to 'PATHOLOGIC_STAGE'.

    • BDH1|622 ,  PCCB|5096 ,  SPP2|6694 ,  TMPRSS6|164656 ,  LCAT|3931 ,  ...

  • 30 genes correlated to 'PATHOLOGY_T_STAGE'.

    • BDH1|622 ,  PCCB|5096 ,  SERPINF2|5345 ,  DHRS1|115817 ,  RGN|9104 ,  ...

  • 13 genes correlated to 'GENDER'.

    • HDHD1A|8226 ,  NCRNA00183|554203 ,  CUX2|23316 ,  SDCBP|6386 ,  GGH|8836 ,  ...

  • 30 genes correlated to 'HISTOLOGICAL_TYPE'.

    • KCND1|3750 ,  HOXB3|3213 ,  C2ORF63|130162 ,  ABR|29 ,  LOC100130776|100130776 ,  ...

  • 1 gene correlated to 'RESIDUAL_TUMOR'.

    • DDTL|100037417

  • 30 genes correlated to 'RACE'.

    • XKR9|389668 ,  PPM1K|152926 ,  TSPAN10|83882 ,  CYP2D6|1565 ,  POM121L10P|646074 ,  ...

  • No genes correlated to 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'RADIATION_THERAPY', 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=13 younger N=17
PATHOLOGIC_STAGE Kruskal-Wallis test N=30        
PATHOLOGY_T_STAGE Spearman correlation test N=30 higher stage N=6 lower stage N=24
PATHOLOGY_N_STAGE Wilcoxon test   N=0        
PATHOLOGY_M_STAGE Wilcoxon test   N=0        
GENDER Wilcoxon test N=13 male N=13 female N=0
RADIATION_THERAPY Wilcoxon test   N=0        
HISTOLOGICAL_TYPE Kruskal-Wallis test N=30        
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) 0-120.8 (median=19.6)
  censored N = 241
  death N = 129
     
  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
UCK2|7371 8.36e-09 0.00015 0.66
SFPQ|6421 3.37e-08 0.00028 0.661
CLEC3B|7123 4.69e-08 0.00028 0.33
GTPBP4|23560 8.12e-08 0.00036 0.66
CAD|790 1.22e-07 0.00043 0.645
RBP4|5950 1.74e-07 0.00051 0.375
G6PD|2539 3.97e-07 0.00098 0.655
CBX2|84733 4.61e-07 0.00098 0.638
TRMT6|51605 4.98e-07 0.00098 0.622
KPNA2|3838 6.79e-07 0.0011 0.672
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) 59.26 (13)
  Significant markers N = 30
  pos. correlated 13
  neg. correlated 17
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
CDCA7|83879 -0.3606 1.118e-12 1.98e-08
EPCAM|4072 -0.3416 2.915e-11 2.59e-07
RAB3D|9545 -0.3153 6.461e-10 3.82e-06
PTK7|5754 -0.3124 9.472e-10 4.2e-06
OSGIN1|29948 0.3103 1.237e-09 4.39e-06
FAM186B|84070 0.2926 1.224e-08 3.62e-05
CES1|1066 0.2816 4.074e-08 8.67e-05
PCM1|5108 -0.2814 4.171e-08 8.67e-05
PEG3|5178 -0.2817 4.399e-08 8.67e-05
FZD9|8326 -0.2985 5.751e-08 0.000102
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 171
  STAGE II 86
  STAGE III 3
  STAGE IIIA 65
  STAGE IIIB 8
  STAGE IIIC 9
  STAGE IV 2
  STAGE IVA 1
  STAGE IVB 2
     
  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
BDH1|622 7.085e-07 0.0126
PCCB|5096 2.58e-06 0.0191
SPP2|6694 3.232e-06 0.0191
TMPRSS6|164656 5.439e-06 0.0241
LCAT|3931 1.146e-05 0.0338
RGN|9104 1.443e-05 0.0338
SRL|6345 1.548e-05 0.0338
F2|2147 1.745e-05 0.0338
RAMP3|10268 1.814e-05 0.0338
CLEC3B|7123 1.902e-05 0.0338
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) 1.8 (0.9)
  N
  T1 181
  T2 94
  T3 80
  T4 13
     
  Significant markers N = 30
  pos. correlated 6
  neg. correlated 24
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
BDH1|622 -0.3239 1.967e-10 3.49e-06
PCCB|5096 -0.3147 6.646e-10 5.9e-06
SERPINF2|5345 -0.2895 1.553e-08 5.68e-05
DHRS1|115817 -0.2885 1.733e-08 5.68e-05
RGN|9104 -0.2879 1.876e-08 5.68e-05
FTCD|10841 -0.2877 1.922e-08 5.68e-05
F2|2147 -0.2856 2.44e-08 5.86e-05
HPX|3263 -0.285 2.643e-08 5.86e-05
CLEC3B|7123 -0.2825 3.499e-08 6.67e-05
C7ORF68|29923 0.2819 3.761e-08 6.67e-05
Clinical variable #5: 'PATHOLOGY_N_STAGE'

No gene related to 'PATHOLOGY_N_STAGE'.

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

PATHOLOGY_N_STAGE Labels N
  N0 252
  N1 4
     
  Significant markers N = 0
Clinical variable #6: 'PATHOLOGY_M_STAGE'

No gene related to 'PATHOLOGY_M_STAGE'.

Table S10.  Basic characteristics of clinical feature: 'PATHOLOGY_M_STAGE'

PATHOLOGY_M_STAGE Labels N
  class0 266
  class1 4
     
  Significant markers N = 0
Clinical variable #7: 'GENDER'

13 genes related to 'GENDER'.

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

GENDER Labels N
  FEMALE 121
  MALE 250
     
  Significant markers N = 13
  Higher in MALE 13
  Higher in FEMALE 0
List of top 10 genes differentially expressed by 'GENDER'

Table S12.  Get Full Table List of top 10 genes differentially expressed by 'GENDER'. 17 significant gene(s) located in sex chromosomes is(are) filtered out.

W(pos if higher in 'MALE') wilcoxontestP Q AUC
HDHD1A|8226 5578 6.313e-23 1.02e-19 0.8156
NCRNA00183|554203 7376 1.229e-15 1.68e-12 0.7562
CUX2|23316 21642 1.57e-12 1.55e-09 0.7272
SDCBP|6386 21882 3.012e-12 2.67e-09 0.7234
GGH|8836 21807 5.211e-12 4.4e-09 0.7209
ABCB1|5243 21777 6.478e-12 5.22e-09 0.7199
CYORF15A|246126 4195 1.851e-11 1.43e-08 0.9871
CYORF15B|84663 4190 2.069e-11 1.53e-08 0.9859
NCK2|8440 8947 1.78e-10 1.26e-07 0.7042
MRPS28|28957 21130 5.625e-10 3.7e-07 0.6985
Clinical variable #8: 'RADIATION_THERAPY'

No gene related to 'RADIATION_THERAPY'.

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

RADIATION_THERAPY Labels N
  NO 339
  YES 9
     
  Significant markers N = 0
Clinical variable #9: 'HISTOLOGICAL_TYPE'

30 genes related to 'HISTOLOGICAL_TYPE'.

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

HISTOLOGICAL_TYPE Labels N
  FIBROLAMELLAR CARCINOMA 3
  HEPATOCELLULAR CARCINOMA 361
  HEPATOCHOLANGIOCARCINOMA (MIXED) 7
     
  Significant markers N = 30
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'

kruskal_wallis_P Q
KCND1|3750 8.415e-06 0.0235
HOXB3|3213 9.321e-06 0.0235
C2ORF63|130162 9.403e-06 0.0235
ABR|29 1.207e-05 0.0235
LOC100130776|100130776 1.596e-05 0.0235
FCHO1|23149 2.25e-05 0.0235
AQP11|282679 2.651e-05 0.0235
PDE3B|5140 2.697e-05 0.0235
TPM4|7171 2.711e-05 0.0235
CACNB3|784 2.716e-05 0.0235
Clinical variable #10: 'RESIDUAL_TUMOR'

One gene related to 'RESIDUAL_TUMOR'.

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

RESIDUAL_TUMOR Labels N
  R0 324
  R1 17
  R2 1
  RX 22
     
  Significant markers N = 1
List of one gene differentially expressed by 'RESIDUAL_TUMOR'

Table S17.  Get Full Table List of one gene differentially expressed by 'RESIDUAL_TUMOR'

kruskal_wallis_P Q
DDTL|100037417 3.267e-06 0.058
Clinical variable #11: 'RACE'

30 genes related to 'RACE'.

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

RACE Labels N
  AMERICAN INDIAN OR ALASKA NATIVE 2
  ASIAN 158
  BLACK OR AFRICAN AMERICAN 17
  WHITE 184
     
  Significant markers N = 30
List of top 10 genes differentially expressed by 'RACE'

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

kruskal_wallis_P Q
XKR9|389668 8.343e-21 1.48e-16
PPM1K|152926 1.569e-16 1.35e-12
TSPAN10|83882 2.29e-16 1.35e-12
CYP2D6|1565 5.605e-16 2.49e-12
POM121L10P|646074 2.281e-14 8.09e-11
FAM128A|653784 3.563e-14 1.05e-10
THOC3|84321 4.568e-14 1.16e-10
LOC162632|162632 6.083e-13 1.3e-09
SIRPB2|284759 6.613e-13 1.3e-09
PRSS53|339105 1.762e-11 2.99e-08
Clinical variable #12: 'ETHNICITY'

No gene related to 'ETHNICITY'.

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

ETHNICITY Labels N
  HISPANIC OR LATINO 18
  NOT HISPANIC OR LATINO 334
     
  Significant markers N = 0
Methods & Data
Input
  • Expresson data file = LIHC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

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

  • Number of patients = 371

  • Number of genes = 17745

  • Number of clinical features = 12

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)