Bioinformatics analysis of long non-coding RNAs in oral premalignant lesions using microarray profiling
Oral premalignant lesions (OPLs) frequently progress from mild-to-severe dysplasia to invasive oral squamous cell carcinoma.This study aims to identify the differentially expressed genes (DEGs) and long non-coding RNAs (lncRNAs)in the OPLs.Datasets GSE31021 (OPLs)and GSE8127 (normal oral mucosa tissue) were downloaded from GEO (Gene Expression Omnibus).DEGs and differentially expressed lncRNAs were identified using LIMMA package in R language followed by false discovery rate (FDR) adjustment with Benjamini and Hochberg method using the package multtest.The screening criteria were FDR < 0.05 and |log2Fq >0.585.The target genes of lncRNAs were predicated among screened DEGs using Pearson”s correlation coefficient.GO function and KEGG pathway analysis were performed for target genes of lncRNAs.A total of 674 DEGs and differentially expressed lncRNAs were screened in OPLs.The 32 interactions of 10 lncRNAs and 524 target genes were predicted.The lncRNA NEAT1 was identified among the top 10 lncRNAs.The co-regulated target genes RP4-684O24, RP11-283I3 and RP11-350G8 were significantly enriched in immune response and mannosyl-oligosaccharide mannosidase activity.The target genes co-regulated by LINC00665and MIR378D2 were significantly enriched in ubiquitin-dependent protein catabolic process,ubiquitin-protein ligase activity and neurotrophin signaling pathway.The lncRNA NEAT1 may play an important role in OPLs.The lncRNA and DEGs identified in OPLs may mediate immune response and neurotrophin signaling, and exhibit ubiquitin ligase activity.The results provide a standard of reference for the role of lncRNAs in early diagnosis of OPLs.
oral cancer oral premalignant lesions differentially expressed genes differentially expressed lncRNAs GO KEGG
Hongcheng Jia Xuan Wang Zheng Sun
Department of Oral Medicine, Beijing Stomatological Hospital, Capital Medical University,Beijing 100 Department of Stomatology, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, Chi Department of Oral Medicine, Beijing Stomatological Hospital, Capital Medical University,Beijing 100
国内会议
北京
英文
156-168
2016-12-16（万方平台首次上网日期，不代表论文的发表时间）