LUAD/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 17814 genes and 4 clinical features across 25 samples, statistically thresholded by P value <= 0.05 and Q value <= 0.25

  • 1 gene correlated to 'GENDER'.

    • MRPL3

  • 1 gene correlated to 'PATHOLOGY.T'.

    • PAPPA2

  • No genes correlated to 'AGE', and 'PATHOLOGY.N'.

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
AGE Spearman correlation test   N=0        
GENDER t test N=1 male N=1 female N=0
PATHOLOGY T Spearman correlation test N=1 higher pT N=0 lower pT N=1
PATHOLOGY N Spearman correlation test   N=0        
Clinical variable #1: 'AGE'

No gene related to 'AGE'.

Table 2.  Basic characteristics of clinical feature: 'AGE'

AGE Mean (SD) 64.16 (10)
  Significant markers N = 0
Clinical variable #2: 'GENDER'

One gene related to 'GENDER'.

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

GENDER Labels N
  FEMALE 12
  MALE 13
     
  Significant markers N = 1
  Higher in MALE 1
  Higher in FEMALE 0
List of one gene differentially expressed by 'GENDER'

Table 4.  Get Full Table List of one gene differentially expressed by 'GENDER'

T ttestP Q AUC
MRPL3 5.51 1.318e-05 0.235 0.9487

Figure 1.  Get High-res Image As an example, this figure shows the association of MRPL3 to 'GENDER'. P value = 1.32e-05 with T-test analysis.

Clinical variable #3: 'PATHOLOGY.T'

One gene related to 'PATHOLOGY.T'.

Table 5.  Basic characteristics of clinical feature: 'PATHOLOGY.T'

PATHOLOGY.T Mean (SD) 1.71 (0.55)
  N
  T1 8
  T2 15
  T3 1
     
  Significant markers N = 1
  pos. correlated 0
  neg. correlated 1
List of one gene significantly correlated to 'PATHOLOGY.T' by Spearman correlation test

Table 6.  Get Full Table List of one gene significantly correlated to 'PATHOLOGY.T' by Spearman correlation test

SpearmanCorr corrP Q
PAPPA2 -0.766 1.28e-05 0.228

Figure 2.  Get High-res Image As an example, this figure shows the association of PAPPA2 to 'PATHOLOGY.T'. P value = 1.28e-05 with Spearman correlation analysis.

Clinical variable #4: 'PATHOLOGY.N'

No gene related to 'PATHOLOGY.N'.

Table 7.  Basic characteristics of clinical feature: 'PATHOLOGY.N'

PATHOLOGY.N Mean (SD) 0.52 (0.79)
  N
  N0 15
  N1 4
  N2 4
     
  Significant markers N = 0
Methods & Data
Input

Input Data

  • Expresson data file = LUAD.medianexp.txt

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

  • Number of samples = 25

  • Number of genes = 17814

  • Number of clinical features = 4

  • p value cutoff = 0.05

  • q value cutoff = 0.25