Identification of an early diagnostic biomarker of lung adenocarcinoma based on co-expression similarity and construction of a diagnostic model

Journal of Translational Medicine
Zhirui FanJie Zhao

Abstract

The purpose of this study was to achieve early and accurate diagnosis of lung cancer and long-term monitoring of the therapeutic response. We downloaded GSE20189 from GEO database as analysis data. We also downloaded human lung adenocarcinoma RNA-seq transcriptome expression data from the TCGA database as validation data. Finally, the expression of all of the genes underwent z test normalization. We used ANOVA to identify differentially expressed genes specific to each stage, as well as the intersection between them. Two methods, correlation analysis and co-expression network analysis, were used to compare the expression patterns and topological properties of each stage. Using the functional quantification algorithm, we evaluated the functional level of each significantly enriched biological function under different stages. A machine-learning algorithm was used to screen out significant functions as features and to establish an early diagnosis model. Finally, survival analysis was used to verify the correlation between the outcome and the biomarkers that we found. We screened 12 significant biomarkers that could distinguish lung cancer patients with diverse risks. Patients carrying variations in these 12 genes also presented a ...Continue Reading

References

Nov 15, 2001·Proceedings of the National Academy of Sciences of the United States of America·A BhattacharjeeM Meyerson
Oct 27, 2006·The New England Journal of Medicine·UNKNOWN International Early Lung Cancer Action Program InvestigatorsOlli S Miettinen
Oct 23, 2008·Nucleic Acids Research·Tanya BarrettRon Edgar
Jan 2, 2009·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Paul RoepmanNico van Zandwijk
Apr 21, 2009·Biotechnology and Bioengineering·Hojung NamDoheon Lee
May 22, 2009·Journal of Thoracic Oncology : Official Publication of the International Association for the Study of Lung Cancer·Kari ChanskyUNKNOWN International Staging Committee and Participating Institutions
Dec 5, 2009·Molecular & Cellular Proteomics : MCP·Gabriel OstlundErik L L Sonnhammer
Mar 18, 2010·Journal of the National Cancer Institute·Jyothi Subramanian, Richard Simon
Feb 13, 2013·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Joan H SchillerEverett E Vokes
Dec 7, 2014·Briefings in Bioinformatics·Sanghamitra BandyopadhyayUjjwal Maulik
Apr 2, 2015·Nucleic Acids Research·Jacob J Hughey, Atul J Butte
Sep 30, 2015·Lung Cancer : Journal of the International Association for the Study of Lung Cancer·Yoshikane YamauchiHans Hoffmann
Oct 31, 2016·Lung Cancer : Journal of the International Association for the Study of Lung Cancer·Beatrice AraminiUliano Morandi
Nov 17, 2017·Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology·Yanding ZhaoChao Cheng
Nov 25, 2017·Robotics and Biomimetics·Satoshi MiuraMasakatsu G Fujie
Nov 29, 2017·PloS One·Manuela HummelAnnette Kopp-Schneider
Dec 2, 2017·International Journal of Cancer. Journal International Du Cancer·Yuzhuo WangHongbing Shen
Dec 2, 2017·Hepatology : Official Journal of the American Association for the Study of Liver Diseases·Avishek Kumar SinghShiv Kumar Sarin
Jan 31, 2018·The Journal of Craniofacial Surgery·Haidong Li, Tao Song

❮ Previous
Next ❯

Citations

Jul 30, 2021·PeerJ. Computer Science·Jose Liñares-BlancoCarlos Fernandez-Lozano
Sep 24, 2021·BMC Bioinformatics·Francisco Carrillo-PerezLuis Javier Herrera

❮ Previous
Next ❯

Datasets Mentioned

BETA
GSE20189

Methods Mentioned

BETA
X-ray
biopsy
chips
RNA-seq

Software Mentioned

Cytoscape
limma

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.