Differential expression patterns of housekeeping genes increase diagnostic and prognostic value in lung cancer

PeerJ
Yu-Chun ChangLi-Li Hsiao

Abstract

Using DNA microarrays, we previously identified 451 genes expressed in 19 different human tissues. Although ubiquitously expressed, the variable expression patterns of these "housekeeping genes" (HKGs) could separate one normal human tissue type from another. Current focus on identifying "specific disease markers" is problematic as single gene expression in a given sample represents the specific cellular states of the sample at the time of collection. In this study, we examine the diagnostic and prognostic potential of the variable expressions of HKGs in lung cancers. Microarray and RNA-seq data for normal lungs, lung adenocarcinomas (AD), squamous cell carcinomas of the lung (SQCLC), and small cell carcinomas of the lung (SCLC) were collected from online databases. Using 374 of 451 HKGs, differentially expressed genes between pairs of sample types were determined via two-sided, homoscedastic t-test. Principal component analysis and hierarchical clustering classified normal lung and lung cancers subtypes according to relative gene expression variations. We used uni- and multi-variate cox-regressions to identify significant predictors of overall survival in AD patients. Classifying genes were selected using a set of training sam...Continue Reading

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Citations

Aug 11, 2018·Molecular Therapy. Methods & Clinical Development·Aisha A AlJanahiCynthia E Dunbar

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Datasets Mentioned

BETA
GDS3257
GSE13213

Methods Mentioned

BETA
RNA-Seq
PCA
GTPase

Software Mentioned

Affymetrix
SPSS
gcRMA
Affymetrix Microarray Suite ( MAS )
RMA
R package
GENE
Excel

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