Opportunities and methods for studying alternative splicing in cancer with RNA-Seq

Huijuan Feng; Zhiyi Qin; Xuegong Zhang

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Opportunities and methods for studying alternative splicing in cancer with RNA-Seq

机译：RNA-SEQ研究癌症替代剪接的机遇和方法

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The biogenesis, development and metastases of cancer are associated with many variations in the tran-scriptome. Alternative splicing of genes is a major post-transcriptional regulation mechanism that is involved in many types of cancer. The next-generation sequencing applied on RNAs (RNA-Seq) provides a new technology for studying transcriptomes. It provides an unprecedented opportunity for quantitatively studying alternative splicing in a systematic way. This mini-review summarizes the current RNA-Seq studies on cancer transcriptomes especially studies on cancer-related alternative splicing, and discusses the strategy for quantitative study of alternative splicing in cancers with RNA-Seq, the bioinformatics methods available and existing questions.

机译：癌症的生物发生，发育和转移与Tran-Scriptome的许多变化相关。基因的替代剪接是涉及许多类型的癌症的主要转录后调节机制。在RNA（RNA-SEQ）上应用的下一代测序提供了一种用于研究转录om的新技术。它提供了一个前所未有的机会，用于以系统的方式定量研究替代拼接。这种迷你审查总结了目前的RNA-SEQ研究转录瘤的研究尤其是关于癌症相关的替代剪接的研究，并讨论了具有RNA-SEQ癌症中替代剪接的定量研究的策略，生物信息学方法可用和现有问题。

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来源
《Cancer letters》 |2013年第2期|共13页
作者
Huijuan Feng; Zhiyi Qin; Xuegong Zhang;
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作者单位

Bioinformatics Division/Center for Synthetic and Systems Biology TNLIST and MOE Key Laboratory for;

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原文格式 PDF
正文语种 eng
中图分类肿瘤学;
关键词
RNA-Seq; Alternative splicing; Cancer; Transcriptomes; Bioinformatics;

机译：RNA-SEQ;替代剪接;癌症;转录om;生物信息学;

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专利

1. Opportunities and methods for studying alternative splicing in cancer with RNA-Seq [J] . Huijuan Feng, Zhiyi Qin, Xuegong Zhang Cancer letters . 2014,第2期

机译：利用RNA-Seq研究癌症中的可变剪接的机会和方法
2. Mining Arabidopsis thaliana RNA-seq data with Integrated Genome Browser reveals stress-induced alternative splicing of the putative splicing regulator SR45a. (Special Issue: Methods and applications of next-generation sequencing in botany.) [J] . Gulledge A. A., Roberts A. D., Vora H., American journal of botany . 2012,第2期

机译：使用集成基因组浏览器对拟南芥RNA-seq数据进行的挖掘揭示了推定剪接调节剂SR45a的应力诱导性选择性剪接。（特刊：下一代测序在植物学中的方法和应用。）
3. RNA-seq analysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noncoding RNAs and aberrant alternative splicings [J] . Shancheng Ren, Zhiyu Peng, Jian-Hua Mao, Cell research. . 2012,第5期

机译：在中国人群中对前列腺癌进行RNA-seq分析，可确定复发性基因融合，与癌症相关的长非编码RNA和异常的可变剪接
4. NanoAsPipe: A transcriptome analysis and alternative splicing detection pipeline for MinION long-read RNA-seq [C] . Kan Liu, Shangang Jia, Qian Du, IEEE International Conference on Bioinformatics and Biomedicine . 2017

机译：NanoAsPipe：用于MinION长读RNA序列的转录组分析和替代剪接检测管线
5. The Epigenetic Regulation of Mdig in Cancers and Its Alternative Splicing Induced by Crispr-Cas9 [D] . Zhang, Qian. 2021

机译：CRISPR-CAS9癌症MDIG的表观遗传调节及其替代剪接
6. Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems [O] . Ruolin Liu, Ann E Loraine, Julie A Dickerson 2014

机译：植物系统中使用RNA-seq进行差异性可变剪接检测的计算方法的比较
7. Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems [O] . Liu, Ruolin, Loraine, Ann E., Dickerson, Julie 2014

机译：植物系统中使用RNA-seq进行差异性可变剪接检测的计算方法的比较

Opportunities and methods for studying alternative splicing in cancer with RNA-Seq

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