LUSC/00: Correlation between mRNA expression and clinical
Overview
Introduction

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

Summary

Testing the association between 17931 genes and one clinical feature across 59 samples, statistically thresholded by P value <= 0.05 and Q value <= 0.25

  • 1 gene correlated to 'AGE'.

    • ALS2CR4

  • 13 genes correlated to 'GENDER'.

    • RPS4Y1 ,  RPS4Y2 ,  DDX3Y ,  CYORF15A ,  EIF1AY ,  ...

  • 2 genes correlated to 'PATHOLOGY.N'.

    • ARHGAP10 ,  ACLY

  • No genes correlated to 'Time to Death', and 'PATHOLOGY.T'.

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 <= 0.25.

Clinical feature Statistical test Significant genes Associated with                 Associated with
Time to Death Cox regression test   N=0        
AGE Spearman correlation test N=1 older N=1 younger N=0
GENDER t test N=13 male N=12 female N=1
PATHOLOGY T Spearman correlation test   N=0        
PATHOLOGY N Spearman correlation test N=2 higher pN N=2 lower pN N=0
Clinical variable #1: 'Time to Death'

No gene related to 'Time to Death'.

Table 2.  Basic characteristics of clinical feature: 'Time to Death'

Time to Death Duration (Months) 0.4-122.4 (median=18.2)
  censored N = 33
  event occurred N = 25
     
  Significant markers N = 0
Clinical variable #2: 'AGE'

One gene related to 'AGE'.

Table 3.  Basic characteristics of clinical feature: 'AGE'

AGE Mean (SD) 66.68 (9)
  Significant markers N = 1
  pos. correlated 1
  neg. correlated 0
List of one gene significantly correlated to 'AGE' by Spearman correlation test

Table 4.  Get Full Table List of one gene significantly correlated to 'AGE' by Spearman correlation test

SpearmanCorr corrP Q
ALS2CR4 0.5576 4.488e-06 0.0805

Figure 1.  Get High-res Image As an example, this figure shows the association of ALS2CR4 to 'AGE'. P value = 4.49e-06 with Spearman correlation analysis. The straight line presents the best linear regression.

Clinical variable #3: 'GENDER'

13 genes related to 'GENDER'.

Table 5.  Basic characteristics of clinical feature: 'GENDER'

GENDER Labels N
  FEMALE 20
  MALE 39
     
  Significant markers N = 13
  Higher in MALE 12
  Higher in FEMALE 1
List of top 10 genes differentially expressed by 'GENDER'

Table 6.  Get Full Table List of top 10 genes differentially expressed by 'GENDER'

T ttestP Q AUC
RPS4Y1 25.98 2.772e-27 4.97e-23 1
RPS4Y2 20.55 2.71e-24 4.86e-20 1
DDX3Y 17.96 1.069e-22 1.92e-18 1
CYORF15A 14.07 5.712e-20 1.02e-15 1
EIF1AY 14.94 5.555e-19 9.96e-15 1
JARID1D 13.64 3.143e-18 5.63e-14 0.9974
UTY 11.19 3.503e-15 6.28e-11 0.9859
CYORF15B 10.3 1.501e-14 2.69e-10 0.9731
USP9Y 8.64 7.223e-12 1.29e-07 0.9564
ZFY 8.61 1.007e-11 1.81e-07 0.9718

Figure 2.  Get High-res Image As an example, this figure shows the association of RPS4Y1 to 'GENDER'. P value = 2.77e-27 with T-test analysis.

Clinical variable #4: 'PATHOLOGY.T'

No gene related to 'PATHOLOGY.T'.

Table 7.  Basic characteristics of clinical feature: 'PATHOLOGY.T'

PATHOLOGY.T Mean (SD) 1.98 (0.71)
  N
  T1 12
  T2 39
  T3 5
  T4 3
     
  Significant markers N = 0
Clinical variable #5: 'PATHOLOGY.N'

2 genes related to 'PATHOLOGY.N'.

Table 8.  Basic characteristics of clinical feature: 'PATHOLOGY.N'

PATHOLOGY.N Mean (SD) 0.37 (0.55)
  N
  N0 39
  N1 18
  N2 2
     
  Significant markers N = 2
  pos. correlated 2
  neg. correlated 0
List of 2 genes significantly correlated to 'PATHOLOGY.N' by Spearman correlation test

Table 9.  Get Full Table List of 2 genes significantly correlated to 'PATHOLOGY.N' by Spearman correlation test

SpearmanCorr corrP Q
ARHGAP10 0.5805 1.786e-06 0.032
ACLY 0.5652 3.101e-06 0.0556

Figure 3.  Get High-res Image As an example, this figure shows the association of ARHGAP10 to 'PATHOLOGY.N'. P value = 1.79e-06 with Spearman correlation analysis.

Methods & Data
Input

Input Data

  • Expresson data file = LUSC.medianexp.txt

  • Clinical data file = LUSC.clin.merged.picked.txt

  • Number of samples = 59

  • Number of genes = 17931

  • Number of clinical features = 5

  • p value cutoff = 0.05

  • q value cutoff = 0.25