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Table 3 SLDA COPD classifier gene differential allelic expression (DAE) in bronchial epithelial cell (BEC) or in GTEx lung tissue database

From: RNAseq analysis of bronchial epithelial cells to identify COPD-associated genes and SNPs

 

DAE in BEC

GTEx Lung Tissue (n = 278)

1SNP

MAF

Subjects Assessed (n)

2Heterozygote Subjects with DAE data (n)

3p-value

eQTL

4p-value

KEAP1-rs1048287

0.1

159

30

9.02E-10

KEAP1

5N.R.

CEBPG-rs3745968

0.11

128

17

6.35E-04

CEBPG

N.R.

CAT-rs1049982

0.34

156

52

1.51E-24

CAT

1.95E-08

TP73-rs1801174

0.09

158

27

1.34E-10

TP73

N.R.

  1. Significant p-values indicated in italicized font
  2. 1SNP that served as marker for DAE. SNPs with highest minor allele frequency chosen
  3. 2n = number of subjects for whom each SNP allele was measurable in BEC after filtering to prevent stochastic sampling error. The fraction of gDNA samples with heterozygotes was comparable to that for cDNA samples and both approximated Hardy Weinberg Equilibrium expectations
  4. 3p-value for F-test comparing inter-individual variation in cDNA to inter-individual variation in gDNA samples
  5. 4p-value reported in GTEx database
  6. 5N.R not reported
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BMC Pulmonary Medicine

ISSN: 1471-2466

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