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Article Dans Une Revue Scientific Reports Année : 2022

Weighted correlation network analysis revealed novel long non-coding RNAs for colorectal cancer

Sepideh Chodary Khameneh
  • Fonction : Auteur
Sara Razi
  • Fonction : Auteur
Sara Shamdani
  • Fonction : Auteur
Georges Uzan
Sina Naserian
  • Fonction : Auteur

Résumé

Abstract Colorectal cancer (CRC) is one of the most prevalent cancers worldwide, which after breast, lung and, prostate cancers, is the fourth prevalent cancer in the United States. Long non-coding RNAs (lncRNAs) have an essential role in the pathogenesis of CRC. Therefore, bioinformatics studies on lncRNAs and their target genes have potential importance as novel biomarkers. In the current study, publicly available microarray gene expression data of colorectal cancer (GSE106582) was analyzed with the Limma, Geoquery, Biobase package. Afterward, identified differentially expressed lncRNAs and their target genes were inserted into Weighted correlation network analysis (WGCNA) to obtain modules and hub genes. A total of nine differentially expressed lncRNAs (LINC01018, ITCH-IT, ITPK1-AS1, FOXP1-IT1, FAM238B, PAXIP1-AS1, ATP2B1-AS1, MIR29B2CHG, and SNHG32) were identified using microarray data analysis. The WGCNA has identified several hub genes for black (LMOD3, CDKN2AIPNL, EXO5, ZNF69, BMS1P5, METTL21A, IL17RD, MIGA1, CEP19, FKBP14), blue (CLCA1, GUCA2A, UGT2B17, DSC2, CA1, AQP8, ITLN1, BEST4, KLF4, IQCF6) and turquoise (PAFAH1B1, LMNB1, CACYBP, GLO1, PUM3, POC1A, ASF1B, SDCCAG3, ASNS, PDCD2L) modules. The findings of the current study will help to improve our understanding of CRC. Moreover, the hub genes that we have identified could be considered as possible prognostic/diagnostic biomarkers. This study led to the determination of nine lncRNAs with no previous association with CRC development.

Dates et versions

hal-03853579 , version 1 (15-11-2022)

Identifiants

Citer

Sepideh Chodary Khameneh, Sara Razi, Sara Shamdani, Georges Uzan, Sina Naserian. Weighted correlation network analysis revealed novel long non-coding RNAs for colorectal cancer. Scientific Reports, 2022, 12 (1), pp.2990. ⟨10.1038/s41598-022-06934-w⟩. ⟨hal-03853579⟩
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