Integrated analysis of differential expression and alternative splicing of non-small cell lung cancer based on RNA sequencing.
Integrated analysis of differential expression and alternative splicing of non-small cell lung cancer based on RNA sequencing.
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基于RNA测序的非小细胞肺癌的差异表达和替代剪接的综合分析。
DOI：
10.3892/ol.2017.6300
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发表时间：
2017-08
期刊：
影响因子：
2.9
通讯作者：
Tian H
中科院分区：
文献类型：
--
作者：
Li Z;Zhao K;Tian H
非小细胞肺癌(NSCLC)是最常见的肺癌类型，具有较高的发病率和死亡率。许多诊断和治疗方法的提出，在一定程度上改善了非小细胞肺癌的预后。然而，非小细胞肺癌的发病机制在很大程度上仍不清楚，还需要进一步的研究。在本研究中，非小细胞肺癌的RNA测序数据集从Gene Expression Omnibus()下载。从原始数据中获得的干净读数被映射到加州大学圣克鲁斯大学基于tophat的人类基因组(Hg19)，并通过袖扣组装成转录。通过Cuffdiff和rMATS分别筛选出差异表达(DE)基因和差异选择性剪接(DAS)基因。通过注释、可视化和综合发现数据库(David)获取了显著丰富的基因本体论(GO)术语和《京都百科全书》中的基因和基因组路径。在不同类型的NSCLC标本中发现了不同数量的DE和DAS基因，但获得了一些共同的功能和途径，包括与异常免疫和细胞活动有关的生物学过程。与物质代谢相关的GO术语和途径，包括胰岛素信号通路和氧化磷酸化，在DAS基因而不是DE基因中丰富。对差异表达和选择性剪接的综合分析可能有助于了解NSCLC的发病机制，并有助于其早期诊断和治疗。
Non-small cell lung cancer (NSCLC) is the most common type of lung cancer, with high morbidity and mortality rates. Numerous diagnosis and treatment methods have been proposed, and the prognosis of NSCLC has improved to a certain extent. However, the mechanisms of NSCLC remain largely unknown, and additional studies are required. In the present study, the RNA sequencing dataset of NSCLC was downloaded from the Gene Expression Omnibus (). The clean reads obtained from the raw data were mapped to the University of California Santa Cruz human genome (hg19), based on TopHat, and were assembled into transcripts via Cufflink. The differential expression (DE) and differential alternative splicing (DAS) genes were screened out through Cuffdiff and rMATS, respectively. The significantly enriched gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes pathways were obtained through the Database of Annotation, Visualization and Integrated Discovery (DAVID). Different numbers of DE and DAS genes were identified in different types of NSCLC samples, but a number of common functions and pathways were obtained, including biological processes associated with abnormal immune and cell activity. GO terms and pathways associated with substance metabolism, including the insulin signaling pathway and oxidative phosphorylation, were enriched in DAS genes rather than DE genes. Integrated analysis of differential expression and alternative splicing may be helpful in understanding the mechanisms of NSCLC, in addition to its early diagnosis and treatment.
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影响因子：
4
作者：
He X;Wang J;Li Y
通讯作者：
Li Y
影响因子：
4
作者：
Sang, Yulan;Bi, Xin;Wang, Dongjie
通讯作者：
Wang, Dongjie
影响因子：
3.8
作者：
Bae JR;Lee BD
通讯作者：
Lee BD
DOI：
10.1016/j.amsu.2015.11.003
发表时间：
2016-02
期刊：
Annals of medicine and surgery (2012)
影响因子：
--
作者：
Nakajima Y;Akiyama H;Kinoshita H;Atari M;Fukuhara M;Saito Y;Sakai H;Uramoto H
通讯作者：
Uramoto H
影响因子：
6.6
作者：
Bisognin, Andrea;Pizzini, Silvia;Mandruzzato, Susanna
通讯作者：
Mandruzzato, Susanna