Integrated TCGA analysis implicates lncRNA CTB-193M12.5 as a prognostic factor in lung adenocarcinoma

Cancer Cell International
Xuehai WangChongzhi Gan

Abstract

Lung cancer is a malignant tumor with the highest incidence and mortality around the world. Recent advances in RNA sequencing technology have enabled insights into long non-coding RNAs (lncRNAs), a previously largely overlooked species in dissecting lung cancer pathology. In this study, we used a comprehensive bioinformatics analysis strategy to identify lncRNAs closely associated with lung adenocarcinoma, using the RNA sequencing datasets collected from more than 500 lung adenocarcinoma patients and deposited at The Cancer Genome Atlas (TCGA) database. Differential expression analysis highlighted lncRNAs CTD-2510F5.4 and CTB-193M12.5, both of which were significantly upregulated in cancerous specimens. Moreover, network analyses showed highly correlated expression levels of both lncRNAs with those of differentially expressed protein-coding genes, and suggested central regulatory roles of both lncRNAs in the gene co-expression network. Importantly, expression of CTB-193M12.5 showed strong negative correlation with patient survival. Our study mined existing TCGA datasets for novel factors associated with lung adenocarcinoma, and identified a largely unknown lncRNA as a potential prognostic factor. Further investigation is warran...Continue Reading

References

Oct 4, 2002·Oncogene·Ana I RoblesCurtis C Harris
Dec 4, 2002·Journal of Clinical Pathology·K J Syrjänen
Dec 31, 2008·BMC Bioinformatics·Peter Langfelder, Steve Horvath
Dec 24, 2010·Genome Biology·Alicia OshlackMatthew D Young
Mar 8, 2011·Cell·Douglas Hanahan, Robert A Weinberg
Jun 18, 2011·Journal of Mammary Gland Biology and Neoplasia·Jay P Reddy, Yi Li
Mar 30, 2012·Omics : a Journal of Integrative Biology·Guangchuang YuQing-Yu He
Sep 11, 2012·Nature·UNKNOWN Cancer Genome Atlas Research Network
Apr 17, 2013·Annales d'endocrinologie·Lluis Fajas
Nov 26, 2013·American Journal of Human Genetics·Konstantin PopadinStylianos E Antonarakis
Apr 23, 2014·Lung Cancer : Journal of the International Association for the Study of Lung Cancer·Seon-Sook HanYeon-Mok Oh
Aug 1, 2014·Nature·UNKNOWN Cancer Genome Atlas Research Network
Aug 28, 2014·Biochimica Et Biophysica Acta·Guodong YangLijun Yuan
Oct 10, 2014·Journal of Cellular and Molecular Medicine·Jing ChenLong-Bang Chen
Dec 3, 2014·Cancer Treatment Reviews·Michael J DuffyWilliam M Gallagher
Apr 25, 2015·Nature Communications·Marta MontesAnders H Lund
Sep 28, 2015·Trends in Cell Biology·Gudrun Böhmdorfer, Andrzej T Wierzbicki
Jan 26, 2016·CA: a Cancer Journal for Clinicians·Wanqing ChenJie He
Nov 5, 2016·Journal of Cancer Research and Clinical Oncology·Antonio Carlos de FreitasCarolina Maria Medeiros do Amaral
Jan 6, 2017·CA: a Cancer Journal for Clinicians·Rebecca L SiegelAhmedin Jemal
Aug 20, 2017·Journal of Proteomics·Byong Chul YooJae Kyung Myung

❮ Previous
Next ❯

Citations


❮ Previous
Next ❯

Datasets Mentioned

BETA
GSE50081
AC099850.7
AC026401.7

Methods Mentioned

BETA
RNA-Seq
interaction prediction
biopsies

Software Mentioned

R package clusterProfiler
R package WGCNA
RIblast
WGCNA
R package heatmaps
Cytoscape
clusterProfiler

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.