Rectum Adenocarcinoma: Correlation between mRNAseq expression and clinical features
(primary solid tumor cohort)
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 18106 genes and 9 clinical features across 51 samples, statistically thresholded by Q value < 0.05, 4 clinical features related to at least one genes.

  • 14 genes correlated to 'GENDER'.

    • DDX3Y|8653 ,  ZFY|7544 ,  XIST|7503 ,  EIF1AY|9086 ,  PRKY|5616 ,  ...

  • 1 gene correlated to 'PATHOLOGY.T'.

    • RAMP1|10267

  • 1 gene correlated to 'TUMOR.STAGE'.

    • CYP2E1|1571

  • 47 genes correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

    • GUSBL2|375513 ,  TTC15|51112 ,  GNG3|2785 ,  RMND5B|64777 ,  ZNF608|57507 ,  ...

  • No genes correlated to 'AGE', 'PATHOLOGY.N', 'PATHOLOGICSPREAD(M)', 'COMPLETENESS.OF.RESECTION', and 'NUMBER.OF.LYMPH.NODES'.

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
AGE Spearman correlation test   N=0        
GENDER t test N=14 male N=12 female N=2
PATHOLOGY T Spearman correlation test N=1 higher pT N=1 lower pT N=0
PATHOLOGY N Spearman correlation test   N=0        
PATHOLOGICSPREAD(M) ANOVA test   N=0        
TUMOR STAGE Spearman correlation test N=1 higher stage N=1 lower stage N=0
RADIATIONS RADIATION REGIMENINDICATION t test N=47 yes N=15 no N=32
COMPLETENESS OF RESECTION ANOVA test   N=0        
NUMBER OF LYMPH NODES Spearman correlation test   N=0        
Clinical variable #1: 'AGE'

No gene related to 'AGE'.

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

AGE Mean (SD) 63.33 (12)
  Significant markers N = 0
Clinical variable #2: 'GENDER'

14 genes related to 'GENDER'.

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

GENDER Labels N
  FEMALE 23
  MALE 28
     
  Significant markers N = 14
  Higher in MALE 12
  Higher in FEMALE 2
List of top 10 genes differentially expressed by 'GENDER'

Table S3.  Get Full Table List of top 10 genes differentially expressed by 'GENDER'

T(pos if higher in 'MALE') ttestP Q AUC
DDX3Y|8653 31.09 9.353e-26 1.69e-21 1
ZFY|7544 26.85 3.725e-25 6.74e-21 1
XIST|7503 -19.94 1.177e-24 2.13e-20 1
EIF1AY|9086 24.06 7.095e-22 1.28e-17 1
PRKY|5616 15.42 6.024e-20 1.09e-15 1
USP9Y|8287 22.78 1.041e-18 1.88e-14 1
CYORF15A|246126 19.49 1.387e-18 2.51e-14 1
KDM5D|8284 27.37 5.082e-18 9.19e-14 1
RPS4Y1|6192 17.83 9.967e-17 1.8e-12 1
CYORF15B|84663 15.97 8.844e-15 1.6e-10 1

Figure S1.  Get High-res Image As an example, this figure shows the association of DDX3Y|8653 to 'GENDER'. P value = 9.35e-26 with T-test analysis.

Clinical variable #3: 'PATHOLOGY.T'

One gene related to 'PATHOLOGY.T'.

Table S4.  Basic characteristics of clinical feature: 'PATHOLOGY.T'

PATHOLOGY.T Mean (SD) 2.82 (0.74)
  N
  T1 3
  T2 10
  T3 31
  T4 7
     
  Significant markers N = 1
  pos. correlated 1
  neg. correlated 0
List of one gene significantly correlated to 'PATHOLOGY.T' by Spearman correlation test

Table S5.  Get Full Table List of one gene significantly correlated to 'PATHOLOGY.T' by Spearman correlation test

SpearmanCorr corrP Q
RAMP1|10267 0.6077 2.252e-06 0.0408

Figure S2.  Get High-res Image As an example, this figure shows the association of RAMP1|10267 to 'PATHOLOGY.T'. P value = 2.25e-06 with Spearman correlation analysis.

Clinical variable #4: 'PATHOLOGY.N'

No gene related to 'PATHOLOGY.N'.

Table S6.  Basic characteristics of clinical feature: 'PATHOLOGY.N'

PATHOLOGY.N Mean (SD) 0.73 (0.86)
  N
  N0 26
  N1 10
  N2 13
     
  Significant markers N = 0
Clinical variable #5: 'PATHOLOGICSPREAD(M)'

No gene related to 'PATHOLOGICSPREAD(M)'.

Table S7.  Basic characteristics of clinical feature: 'PATHOLOGICSPREAD(M)'

PATHOLOGICSPREAD(M) Labels N
  M0 37
  M1 4
  M1A 1
  MX 9
     
  Significant markers N = 0
Clinical variable #6: 'TUMOR.STAGE'

One gene related to 'TUMOR.STAGE'.

Table S8.  Basic characteristics of clinical feature: 'TUMOR.STAGE'

TUMOR.STAGE Mean (SD) 2.4 (1)
  N
  Stage 1 11
  Stage 2 14
  Stage 3 16
  Stage 4 7
     
  Significant markers N = 1
  pos. correlated 1
  neg. correlated 0
List of one gene significantly correlated to 'TUMOR.STAGE' by Spearman correlation test

Table S9.  Get Full Table List of one gene significantly correlated to 'TUMOR.STAGE' by Spearman correlation test

SpearmanCorr corrP Q
CYP2E1|1571 0.6766 1.303e-07 0.00236

Figure S3.  Get High-res Image As an example, this figure shows the association of CYP2E1|1571 to 'TUMOR.STAGE'. P value = 1.3e-07 with Spearman correlation analysis.

Clinical variable #7: 'RADIATIONS.RADIATION.REGIMENINDICATION'

47 genes related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

Table S10.  Basic characteristics of clinical feature: 'RADIATIONS.RADIATION.REGIMENINDICATION'

RADIATIONS.RADIATION.REGIMENINDICATION Labels N
  NO 3
  YES 48
     
  Significant markers N = 47
  Higher in YES 15
  Higher in NO 32
List of top 10 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

Table S11.  Get Full Table List of top 10 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

T(pos if higher in 'YES') ttestP Q AUC
GUSBL2|375513 -9.35 2.16e-12 3.57e-08 0.8819
TTC15|51112 8.72 1.792e-11 2.96e-07 0.9028
GNG3|2785 -8.59 3.078e-11 5.09e-07 0.8958
RMND5B|64777 8.67 1.021e-10 1.69e-06 0.9306
ZNF608|57507 8.54 2.098e-10 3.47e-06 0.8958
PAK1IP1|55003 -7.92 5.672e-10 9.38e-06 0.9236
DDX19A|55308 -7.64 7.938e-10 1.31e-05 0.8681
TRA2B|6434 -7.76 2.197e-09 3.63e-05 0.8889
WASH2P|375260 -7.16 3.865e-09 6.39e-05 0.8542
TMEM117|84216 -7.15 4.477e-09 7.4e-05 0.8681

Figure S4.  Get High-res Image As an example, this figure shows the association of GUSBL2|375513 to 'RADIATIONS.RADIATION.REGIMENINDICATION'. P value = 2.16e-12 with T-test analysis.

Clinical variable #8: 'COMPLETENESS.OF.RESECTION'

No gene related to 'COMPLETENESS.OF.RESECTION'.

Table S12.  Basic characteristics of clinical feature: 'COMPLETENESS.OF.RESECTION'

COMPLETENESS.OF.RESECTION Labels N
  R0 35
  R1 1
  RX 3
     
  Significant markers N = 0
Clinical variable #9: 'NUMBER.OF.LYMPH.NODES'

No gene related to 'NUMBER.OF.LYMPH.NODES'.

Table S13.  Basic characteristics of clinical feature: 'NUMBER.OF.LYMPH.NODES'

NUMBER.OF.LYMPH.NODES Mean (SD) 3.33 (6)
  Significant markers N = 0
Methods & Data
Input

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

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

  • Number of patients = 51

  • Number of genes = 18106

  • Number of clinical features = 9

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] Spearman, C, The proof and measurement of association between two things, Amer. J. Psychol 15:72-101 (1904)
[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] Howell, D, Statistical Methods for Psychology. (5th ed.), Duxbury Press:324-5 (2002)
[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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