Comprehensive Analysis of Differentially Expressed lncRNAs in Gastric Cancer

Frontiers in Cell and Developmental Biology
Nan XiaoLiran Juan

Abstract

Gastric cancer (GC) is the fourth most common malignant tumor. The mechanism underlying GC occurrence and development remains unclear. Previous studies have indicated that long non-coding RNAs (lncRNAs) are significantly associated with gastric cancer, but a systematic understanding of the role of lncRNAs in gastric cancer is lacking. In recent years, with the development of next-generation sequencing technology, tens of thousands of lncRNAs have been discovered. However, a large number of unannotated lncRNAs remain unidentified in different tissues, including potential gastric cancer-related lncRNAs. In this study, RNA sequencing (RNA-seq) data from 16 samples of eight gastric cancer patients were obtained and analyzed. A total of 1,854 previously unannotated lncRNAs were identified by ab initio assembly, and 520 differentially expressed lncRNAs were validated in the TCGA expression dataset. Methylation and copy number variation (CNV) array data from the same sample were integrated in the analysis. Changes in DNA methylation levels and CNVs may be responsible for the differential expression of 91 lncRNAs. Differentially expressed lncRNAs were enriched in coexpressed clusters of genes related to functions such as cell signaling...Continue Reading

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Citations

Jan 9, 2021·Briefings in Bioinformatics·Qing-Wen WuChun-Hou Zheng

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Datasets Mentioned

BETA
GSE85467

Methods Mentioned

BETA
RNA-seq
ChIP-seq

Software Mentioned

Cufflinks
Cuffmerge
TopHat
ChipSeeker
ChAMP
GenomicFeatures
Cytoscape
Coding Potential Calculator ( CPC )
R
multtest

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