Identification of mutant genes with high-frequency, high-risk, and high-expression in lung adenocarcinoma

Thoracic Cancer
Guiyuan LiYunqing Mei

Abstract

To identify mutant genes with high-frequency-risk-expression between lung adenocarcinoma and normal samples. The ribonucleic acid RNA-Seq data GSE34914 and GSE37765 were downloaded from the Gene Expression Omnibus database, including 12 lung adenocarcinoma samples and six controls. All RNA-Seq reads were processed and the gene-expression level was calculated. Single nucleotide variation (SNV) was analyzed and the locations of mutant sites were recorded. In addition, the frequency and risk-level of mutant genes were calculated. Gene Ontology (GO) functional analysis was performed. The reported cancer genes were searched in tumor suppressor genes, Cancer Genes, and the Catalogue of Somatic Mutations in Cancer (COSMIC) database. The SNV annotations of somatic mutation sites showed that 70% of mutation sites in the exon region occurred in the coding sequence (CDS). Thyroid hormone receptor interactor (TRIP)12 was identified with the highest frequency. A total of 118 mutant genes with high frequency and high-risk were selected and significantly enriched into several GO terms. No base mutation of cyclin C (CCNC) or RAB11A was recorded. At fragments per kilobase per million reads (FPKM) ≥ 56.5, reported tumor suppressor genes catenin ...Continue Reading

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Feb 12, 2019·ERJ Open Research·Jacob Shujui HsuMaria-Mercè Garcia-Barcelo
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Nov 3, 2020·Experimental and Molecular Pathology·Fang FangLiming Chang

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