Colon/Rectal Adenocarcinoma: Correlation between mRNAseq expression and clinical features
Maintained by Juok Cho (Broad Institute)
Overview
Introduction

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

Summary

Testing the association between 17880 genes and 9 clinical features across 264 samples, statistically thresholded by Q value < 0.05, 7 clinical features related to at least one genes.

  • 120 genes correlated to 'PRIMARY.SITE.OF.DISEASE'.

    • DRD5|1816 ,  H1FX|8971 ,  LOC152217|152217 ,  C2CD4D|100191040 ,  CTU1|90353 ,  ...

  • 32 genes correlated to 'GENDER'.

    • RPS4Y1|6192 ,  ZFY|7544 ,  XIST|7503 ,  DDX3Y|8653 ,  KDM5D|8284 ,  ...

  • 427 genes correlated to 'HISTOLOGICAL.TYPE'.

    • SNHG11|128439 ,  SLC19A3|80704 ,  GTF2IRD1|9569 ,  PLAGL2|5326 ,  POFUT1|23509 ,  ...

  • 1 gene correlated to 'PATHOLOGY.T'.

    • NRG1|3084

  • 1 gene correlated to 'PATHOLOGY.N'.

    • DIRAS2|54769

  • 1 gene correlated to 'PATHOLOGICSPREAD(M)'.

    • GFI1|2672

  • 2 genes correlated to 'TUMOR.STAGE'.

    • GFI1|2672 ,  ENOSF1|55556

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

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=0        
PRIMARY SITE OF DISEASE t test N=120 rectum N=104 colon N=16
GENDER t test N=32 male N=14 female N=18
HISTOLOGICAL TYPE ANOVA test N=427        
PATHOLOGY T Spearman correlation test N=1 higher pT N=0 lower pT N=1
PATHOLOGY N Spearman correlation test N=1 higher pN N=1 lower pN N=0
PATHOLOGICSPREAD(M) ANOVA test N=1        
TUMOR STAGE Spearman correlation test N=2 higher stage N=0 lower stage N=2
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) 0.9-72.1 (median=12)
  censored N = 131
  death N = 20
     
  Significant markers N = 0
Clinical variable #2: 'AGE'

No gene related to 'AGE'.

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

AGE Mean (SD) 68.86 (12)
  Significant markers N = 0
Clinical variable #3: 'PRIMARY.SITE.OF.DISEASE'

120 genes related to 'PRIMARY.SITE.OF.DISEASE'.

Table S3.  Basic characteristics of clinical feature: 'PRIMARY.SITE.OF.DISEASE'

PRIMARY.SITE.OF.DISEASE Labels N
  COLON 191
  RECTUM 71
     
  Significant markers N = 120
  Higher in RECTUM 104
  Higher in COLON 16
List of top 10 genes differentially expressed by 'PRIMARY.SITE.OF.DISEASE'

Table S4.  Get Full Table List of top 10 genes differentially expressed by 'PRIMARY.SITE.OF.DISEASE'

T(pos if higher in 'RECTUM') ttestP Q AUC
DRD5|1816 -7.58 2.08e-11 3.72e-07 0.7857
H1FX|8971 6.83 1.277e-10 2.28e-06 0.7506
LOC152217|152217 6.81 1.606e-10 2.87e-06 0.7414
C2CD4D|100191040 6.82 1.792e-10 3.2e-06 0.7441
CTU1|90353 6.79 2.404e-10 4.3e-06 0.7404
HOXB13|10481 6.93 3.887e-10 6.95e-06 0.78
ANKHD1-EIF4EBP3|404734 6.64 4.925e-10 8.8e-06 0.7398
TMEM160|54958 6.31 2.735e-09 4.89e-05 0.7574
ANKRD9|122416 6.3 4.725e-09 8.44e-05 0.7437
ALKBH6|84964 6.26 5.559e-09 9.93e-05 0.7481

Figure S1.  Get High-res Image As an example, this figure shows the association of DRD5|1816 to 'PRIMARY.SITE.OF.DISEASE'. P value = 2.08e-11 with T-test analysis.

Clinical variable #4: 'GENDER'

32 genes related to 'GENDER'.

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

GENDER Labels N
  FEMALE 132
  MALE 132
     
  Significant markers N = 32
  Higher in MALE 14
  Higher in FEMALE 18
List of top 10 genes differentially expressed by 'GENDER'

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

T(pos if higher in 'MALE') ttestP Q AUC
RPS4Y1|6192 29.28 6.211e-76 1.11e-71 0.9969
ZFY|7544 28.06 7.279e-61 1.3e-56 0.9887
XIST|7503 -25.51 4.986e-59 8.91e-55 0.9867
DDX3Y|8653 28.71 2.332e-53 4.17e-49 0.9949
KDM5D|8284 27.27 1.744e-47 3.12e-43 0.9951
TMSB4Y|9087 21.2 3.22e-46 5.76e-42 0.9675
NLGN4Y|22829 18.43 6.952e-41 1.24e-36 0.9554
PRKY|5616 16.15 8.03e-41 1.44e-36 0.9126
TSIX|9383 -16.55 1.141e-39 2.04e-35 0.9354
CYORF15A|246126 21.5 1.241e-39 2.22e-35 0.9831

Figure S2.  Get High-res Image As an example, this figure shows the association of RPS4Y1|6192 to 'GENDER'. P value = 6.21e-76 with T-test analysis.

Clinical variable #5: 'HISTOLOGICAL.TYPE'

427 genes related to 'HISTOLOGICAL.TYPE'.

Table S7.  Basic characteristics of clinical feature: 'HISTOLOGICAL.TYPE'

HISTOLOGICAL.TYPE Labels N
  COLON ADENOCARCINOMA 162
  COLON MUCINOUS ADENOCARCINOMA 27
  RECTAL ADENOCARCINOMA 60
  RECTAL MUCINOUS ADENOCARCINOMA 8
     
  Significant markers N = 427
List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'

Table S8.  Get Full Table List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'

ANOVA_P Q
SNHG11|128439 5.651e-15 1.01e-10
SLC19A3|80704 2.044e-13 3.65e-09
GTF2IRD1|9569 6.397e-13 1.14e-08
PLAGL2|5326 1.097e-12 1.96e-08
POFUT1|23509 1.632e-12 2.92e-08
NECAB3|63941 2.978e-12 5.32e-08
AGR2|10551 4.07e-12 7.27e-08
FAM46A|55603 4.67e-12 8.35e-08
HOXB13|10481 1.47e-11 2.63e-07
ZSWIM1|90204 1.835e-11 3.28e-07

Figure S3.  Get High-res Image As an example, this figure shows the association of SNHG11|128439 to 'HISTOLOGICAL.TYPE'. P value = 5.65e-15 with ANOVA analysis.

Clinical variable #6: 'PATHOLOGY.T'

One gene related to 'PATHOLOGY.T'.

Table S9.  Basic characteristics of clinical feature: 'PATHOLOGY.T'

PATHOLOGY.T Mean (SD) 2.8 (0.64)
  N
  T1 11
  T2 53
  T3 176
  T4 22
     
  Significant markers N = 1
  pos. correlated 0
  neg. correlated 1
List of one gene significantly correlated to 'PATHOLOGY.T' by Spearman correlation test

Table S10.  Get Full Table List of one gene significantly correlated to 'PATHOLOGY.T' by Spearman correlation test

SpearmanCorr corrP Q
NRG1|3084 -0.2969 1.199e-06 0.0214

Figure S4.  Get High-res Image As an example, this figure shows the association of NRG1|3084 to 'PATHOLOGY.T'. P value = 1.2e-06 with Spearman correlation analysis.

Clinical variable #7: 'PATHOLOGY.N'

One gene related to 'PATHOLOGY.N'.

Table S11.  Basic characteristics of clinical feature: 'PATHOLOGY.N'

PATHOLOGY.N Mean (SD) 0.58 (0.78)
  N
  N0 158
  N1 57
  N2 48
     
  Significant markers N = 1
  pos. correlated 1
  neg. correlated 0
List of one gene significantly correlated to 'PATHOLOGY.N' by Spearman correlation test

Table S12.  Get Full Table List of one gene significantly correlated to 'PATHOLOGY.N' by Spearman correlation test

SpearmanCorr corrP Q
DIRAS2|54769 0.4097 4.54e-07 0.00812

Figure S5.  Get High-res Image As an example, this figure shows the association of DIRAS2|54769 to 'PATHOLOGY.N'. P value = 4.54e-07 with Spearman correlation analysis.

Clinical variable #8: 'PATHOLOGICSPREAD(M)'

One gene related to 'PATHOLOGICSPREAD(M)'.

Table S13.  Basic characteristics of clinical feature: 'PATHOLOGICSPREAD(M)'

PATHOLOGICSPREAD(M) Labels N
  M0 220
  M1 39
  M1A 2
     
  Significant markers N = 1
List of one gene differentially expressed by 'PATHOLOGICSPREAD(M)'

Table S14.  Get Full Table List of one gene differentially expressed by 'PATHOLOGICSPREAD(M)'

ANOVA_P Q
GFI1|2672 1.877e-06 0.0336

Figure S6.  Get High-res Image As an example, this figure shows the association of GFI1|2672 to 'PATHOLOGICSPREAD(M)'. P value = 1.88e-06 with ANOVA analysis.

Clinical variable #9: 'TUMOR.STAGE'

2 genes related to 'TUMOR.STAGE'.

Table S15.  Basic characteristics of clinical feature: 'TUMOR.STAGE'

TUMOR.STAGE Mean (SD) 2.35 (0.97)
  N
  Stage 1 53
  Stage 2 98
  Stage 3 68
  Stage 4 37
     
  Significant markers N = 2
  pos. correlated 0
  neg. correlated 2
List of 2 genes significantly correlated to 'TUMOR.STAGE' by Spearman correlation test

Table S16.  Get Full Table List of 2 genes significantly correlated to 'TUMOR.STAGE' by Spearman correlation test

SpearmanCorr corrP Q
GFI1|2672 -0.3179 2.025e-07 0.00362
ENOSF1|55556 -0.296 1.428e-06 0.0255

Figure S7.  Get High-res Image As an example, this figure shows the association of GFI1|2672 to 'TUMOR.STAGE'. P value = 2.03e-07 with Spearman correlation analysis.

Methods & Data
Input

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

  • Clinical data file = COADREAD-TP.clin.merged.picked.txt

  • Number of patients = 264

  • Number of genes = 17880

  • Number of clinical features = 9

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

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

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

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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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