Weighted gene coexpression network analysis identifies hub genes related to KRAS mutant lung adenocarcinoma
| Autor: | Shuting Han, Dongjun Dai, Xian Wang, Hongchuan Jin, Rongkai Shi |
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| Rok vydání: | 2020 |
| Předmět: |
Male
Lung Neoplasms The Cancer Genome Atlas Adenocarcinoma of Lung Computational biology medicine.disease_cause TMSB10 Proto-Oncogene Proteins p21(ras) 03 medical and health sciences 0302 clinical medicine Ribosomal protein Databases Genetic Quality Improvement Study medicine Biomarkers Tumor Humans Gene Regulatory Networks 030212 general & internal medicine RNA Messenger Gene Regulation of gene expression business.industry Gene Expression Profiling Computational Biology General Medicine medicine.disease Prognosis Survival Analysis KRAS mutant lung adenocarcinoma Gene expression profiling Gene Expression Regulation Neoplastic 030220 oncology & carcinogenesis Mutation Weighted Gene Coexpression Network Analysis ComputingMethodologies_DOCUMENTANDTEXTPROCESSING Adenocarcinoma Female KRAS hub gene business COX6A1 Research Article |
| Zdroj: | Medicine |
| ISSN: | 1536-5964 |
| Popis: | Supplemental Digital Content is available in the text The aim of current study was to use Weighted Gene Coexpression Network Analysis (WGCNA) to identify hub genes related to the incidence and prognosis of KRAS mutant (MT) lung adenocarcinoma (LUAD). We involved 184 stage IIB to IV LUAD samples and 59 normal lung tissue samples from The Cancer Genome Atlas (TCGA) database. The R package “limma” was used to identify differentially expressed genes (DEGs). WGCNA and survival analyses were performed by R packages “WGCNA” and “survival,” respectively. The functional analyses were performed by R package “clusterProfiler” and GSEA software. Network construction and MCODE analysis were performed by Cytoscape_v3.6.1. Totally 2590 KRAS MT specific DEGs were found between LUAD and normal lung tissues, and 10 WGCNA modules were identified. Functional analysis of the key module showed the ribosome biogenesis related terms were enriched. We observed the expression of 8 genes were positively correlated to the worse survival of KRAS MT LUAD patients, the 7 of them were validated by Kaplan–Meier plotter database (kmplot.com/) (thymosin Beta 10 [TMSB10], ribosomal Protein S16 [RPS16], mitochondrial ribosomal protein L27 [MRPL27], cytochrome c oxidase subunit 6A1 [COX6A1], HCLS1-associated protein X-1 [HAX1], ribosomal protein L38 [RPL38], and ATP Synthase Membrane Subunit DAPIT [ATP5MD]). The GSEA analysis found mTOR and STK33 pathways were upregulated in KRAS MT LUAD (P |
| Databáze: | OpenAIRE |
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