Genome-wide Coexpression Dynamics in Lung Adenocarcinoma Open Access

Abstract

Genome-wide Coexpression Dynamics in Lung
Adenocarcinoma
By Pei-Yu Lin
Lung cancer is one of the leading cause of cancer death in the United States and
worldwide. Lung cancer in never smokers is almost universally non-small cell lung
carcinoma (NSCLC), with a sizeable majority being adenocarcinoma. A microarray is
a multiplex lab-on-a-chip consisting of an arrayed series of thousands of microscopic
spots of DNA oligonucleotides that are used to hybridize a cDNA or cRNA sample.
The high- throughput technology can accomplish many genetic tests in parallel and
has dramatically accelerated many types of investigation. Liquid Association (LA) is
a method to systematically study the co-expression pattern between functionally
related genes as the cellular-state changes. In this study we used LA to analyze
NSCLC DNA microarray data from 4 different lung cancer institutes. We found genes
APOL3 and CEACAM1 to be a potential gene pair that exhibit dynamic correlations
for blood glucose level maintenance when using CMKLR1 as the surrogate of the
cellular-status. A study from Sergentanis et al. pointed out that the defect of glucose
metabolism is a meaningful factor to elevate lung cancer risk. Our result on the
potential dynamic correlation of genes APOL3 and CEACAM1 could provide
biologists and doctors candidate genes for further study of the relationship between
glucose metabolism and lung cancer formation.

Table of Contents

Table of contents

Introduction .................................................................................................................... 1
Lung cancer ............................................................................................................ 1
DNA Microarray .................................................................................................... 2
Theoretical Concepts ............................................................................................. 3
Study Goal ............................................................................................................. 5
Data Description .................................................................................................... 5
Methods.......................................................................................................................... 7
Gene filtering ......................................................................................................... 7
Gene selection ........................................................................................................ 8
Results .......................................................................................................................... 12
Two gene pairs were selected by Liquid Association .......................................... 12
Interpretation of significant finding ..................................................................... 13
Discussion .................................................................................................................... 18
Table 1. Summary statistics of the clinical and survival data ...................................... 22
Figure 1. The flow chart of analysis procedure ........................................................... 23
Figure 2. Co-expression dynamics. .............................................................................. 24
Reference ..................................................................................................................... 25

About this Master's Thesis

Rights statement

• Permission granted by the author to include this thesis or dissertation in this repository. All rights reserved by the author. Please contact the author for information regarding the reproduction and use of this thesis or dissertation.

School	Rollins School of Public Health
Department	Biostatistics and Bioinformatics
Subfield / Discipline	Biostatistics - MPH & MSPH
Degree	MSPH
Submission	Master's Thesis
Language	English
Research Field	Biology, Biostatistics
Keyword	liquid association
Committee Chair / Thesis Advisor	Yu, Tianwei, Emory University
Committee Members	Wu, Hao, Emory University
Partnering Agencies	Does not apply (no collaborating organization)

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