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基于高通量RNA-Seq数据的水稻转录组重构建与分析.pdf55页
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水稻是我国最重要的粮食作物之一，全国水稻种植面积约占粮食作物总种植面积的
30%，产量接近全国粮食总产量的一半。同时，水稻也是一种十分重要的模式生物。水
稻主要有两个亚种，黏性、短粒的粳稻（japonica ），和非粘性、长粒的籼稻（indica ），
而现有对水稻的研究主要针对粳稻。
近年来，随着高通量测序技术在转录组水平的逐渐发展与应用，RNA-Seq 技术也为
转录组结构的解析提供了全新的技术支撑。过去几年间，出现了多种针对转录组复杂性
的研究方法，如基因表达丰度、可变剪切、等位基因特异性表达、RNA 编辑、基因融合。
目前，国内外相关科研机构也越来越多的使用RNA-Seq
数据对水稻转录组进行扩
充，注释了大量的水稻全新的转录活跃区域，并对大量发现的区域进行了RT-PCR 鉴定，
以及编码性分析，并扩充了基因边界。此外，还有研究小组针对水稻的不同发育阶段，
对水稻胚胎进行了测序，统计了每个时间段的基因表达情况，统计了所有表达基因的分
布、覆盖度分布，统计了不同发育阶段基因的特意表达情况，并对不同生长阶段表达的
基因进行了详细的基因特异性表达分析。
本研究以水稻转录组重建与功能性分析为目标，进行了水稻 RNA-Seq
数据收集、
数据质量评估、转录组重建的分析流程构造和优化、并最终水稻的转录组未注释转录活
跃区域进行了较为全面的分析。其中，总共收集到可使用的总共得到 19 个非生物学重
复的样本，来自 21
个文库的 mRNA-Seq
数据。最终，我们在水稻转录组中鉴定到了
100478 个全新剪切位点，并且探测到RAP-DB 注释的82.84% 的剪切位点。接着，我们
正在加载中，请稍后...MapSplice: accurate mapping of RNA-seq reads for splice junction discoveryNucleic Acids ResK. Wang& D. Singh& Z. Zeng& S. J. Coleman& Y. Huang ... J. Liu
The accurate mapping of reads that span splice junctions is a critical component of all analytic techniques that work with RNA-seq data. We introduce a second generation splice detection algorithm, MapSplice, whose focus is high sensitivity and specificity in the detection of splices as well as CPU and memory efficiency. MapSplice can be applied to both short (& 75 bp) and long reads (&= 75 bp). MapSplice is not dependent on splice site features or intron length, consequently it can detect novel canonical as well as non-canonical splices. MapSplice leverages the quality and diversity of read alignments of a given splice to increase accuracy. We demonstrate that MapSplice achieves higher sensitivity and specificity than TopHat and SpliceMap on a set of simulated RNA-seq data. Experimental studies also support the accuracy of the algorithm. Splice junctions derived from eight breast cancer RNA-seq datasets recapitulated the extensiveness of alternative splicing on a global level as well as the differences between molecular subtypes of breast cancer. These combined results indicate that MapSplice is a highly accurate algorithm for the alignment of RNA-seq reads to splice junctions. Software download URL: http://www.netlab.uky.edu/p/bioinfo/MapSplice.
MapSplice：准确比对RNA-seq片段以进行剪接点发现
跨剪接点片段（reads）的准确比对是处理RNA-seq数据的所有分析技术的一个关键部件。我们介绍了一个第二代剪接检测算法，MapSplice，它的焦点是在剪接检测中的高敏感性和特异性，以及CPU和内存高效。MapSplice能够应用到短片段（& 75 bp）和长片段（&= 75 bp）。MapSplice不依赖于剪接位点特征或内含子长度，因此，它能够检测新的典型剪接以及非典型剪接。MapSplice利用一个给定剪接片段比对的质量和多样性以增加准确性。我们证明在一套模拟RNA-seq数据上，MapSplice获得了比TopHat和SpliceMap更高的敏感性和特异性。实验研究也支持该算法的准确性。源自8个乳腺癌RNA-seq数据集的剪接点在一个全局水平上概括了选择性剪接的可扩展性，以及乳腺癌分子亚型间的差异。这些合并的结果表明MapSplice是发现剪接点的一种高度准确的RNA-seq片段比对算法。软件下载URL：http://www.netlab.uky.edu/p/bioinfo/MapSplice。
http://dx.doi.org/10.1093/nar/gkq622http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2952873/pdf/gkq622.pdf1, Alternative isoform regulation in human tissue transcriptomes []
2, Regulation of alternative splicing by histone modifications []
3, A conserved alternative splice in the von Recklinghausen neurofibromatosis (NF1) gene produces two neurofibromin isoforms, both of which have GTPase-activating protein activity []
4, Genomic structure of DNA encoding the lymphocyte homing receptor CD44 reveals at least 12 alternatively spliced exons []
5, Genome-wide analysis of transcript isoform variation in humans []
6, FGFR2 exon IIIa and IIIc mutations in Crouzon, Jackson-Weiss, and Pfeiffer syndromes: evidence for missense changes, insertions, and a deletion due to alternative RNA splicing []
7, Frequent activating FGFR2 mutations in endometrial carcinomas parallel germline mutations associated with craniosynostosis and skeletal dysplasia syndromes []
8, Molecular portraits of human breast tumours []
9, Drug-sensitive FGFR2 mutations in endometrial carcinoma []
10, Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays []
11, Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform []
12, Nova regulates brain-specific splicing to shape the synapse []
13, Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines []
14, Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing []
15, Mapping and quantifying mammalian transcriptomes by RNA-Seq []
16, A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome []
17, Analysis of splicing patterns by pyrosequencing []
18, An expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs []
19, Statistical inferences for isoform expression in RNA-Seq []
20, Optimal spliced alignments of short sequence reads []
21, TopHat: discovering splice junctions with RNA-Seq []
22, Detection of splice junctions from paired-end RNA-seq data by SpliceMap []
23, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome []
24, Fast and accurate short read alignment with Burrows-Wheeler transform []
25, SOAP2: an improved ultrafast tool for short read alignment []
26, BFAST: an alignment tool for large scale genome resequencing []
27, Mapping short DNA sequencing reads and calling variants using mapping quality scores []
28, The effect of sequence quality on sequence alignment []
29, ASTD: The Alternative Splicing and Transcript Diversity database []
30, Improved base calling for the Illumina Genome Analyzer using machine learning strategies []
31, The multiple functions of Numb []
32, Splicing graphs and EST assembly problem []
33, Reconstruction of full-length isoforms from splice graphs []
34, De novo transcriptome assembly with ABySS []
35, A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level []
36, Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments []
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