MeDAS: a Metazoan Developmental Alternative Splicing database.
MeDAS: a Metazoan Developmental Alternative Splicing database.
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DOI：
10.1093/nar/gkaa886
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发表时间：
2021-01-08
影响因子：
14.9
通讯作者：
Chen L
中科院分区：
文献类型：
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作者：
Li Z;Zhang Y;Bush SJ;Tang C;Chen L;Zhang D;Urrutia AO;Lin JW;Chen L
选择性剪接在真核生物基因组中广泛存在，并极大地增加了转录组的多样性。许多替代异构体在发育过程中具有功能性作用，并且在时间上受到精确调节。为了促进在发育背景下的选择性剪接的研究，我们创建了MeDAS，一个后生动物发育选择性剪接数据库。MeDAS是一种增值资源，它重新分析公开存档的RNA-seq文库，以提供关于可变剪接事件的定量数据，因为它们在发展的时间过程中会发生变化。它具有广泛的时间和分类范围，旨在帮助用户在整个发展过程中确定选择性剪接的趋势。为了创建MeDAS，我们重新分析了一组2232个Illumina polyA+ RNA-seq文库，这些文库绘制了18个物种胚胎和出生后发育的详细时间过程，其分类范围涵盖了从秀丽隐杆线虫到人类的主要后生动物谱系。MeDAS可在https://das.chenlulab.com上免费获得，既可作为原始数据表，也可作为交互式浏览器，允许按物种、组织或基因组特征（基因、转录本或外显子ID和序列）进行搜索。结果将提供关于针对查询特征识别的选择性剪接事件的细节，并且可以分别在基因、转录本和外显子水平上可视化为表达和包含水平的时间过程。
Alternative splicing is widespread throughout eukaryotic genomes and greatly increases transcriptomic diversity. Many alternative isoforms have functional roles in developmental processes and are precisely temporally regulated. To facilitate the study of alternative splicing in a developmental context, we created MeDAS, a Metazoan Developmental Alternative Splicing database. MeDAS is an added-value resource that re-analyses publicly archived RNA-seq libraries to provide quantitative data on alternative splicing events as they vary across the time course of development. It has broad temporal and taxonomic scope and is intended to assist the user in identifying trends in alternative splicing throughout development. To create MeDAS, we re-analysed a curated set of 2232 Illumina polyA+ RNA-seq libraries that chart detailed time courses of embryonic and post-natal development across 18 species with a taxonomic range spanning the major metazoan lineages from Caenorhabditis elegans to human. MeDAS is freely available at https://das.chenlulab.com both as raw data tables and as an interactive browser allowing searches by species, tissue, or genomic feature (gene, transcript or exon ID and sequence). Results will provide details on alternative splicing events identified for the queried feature and can be visualised at the gene-, transcript- and exon-level as time courses of expression and inclusion levels, respectively.
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DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
影响因子：
14.9
作者：
NCBI Resource Coordinators
通讯作者：
NCBI Resource Coordinators
影响因子：
12.3
作者：
McIntyre LM;Bono LM;Genissel A;Westerman R;Junk D;Telonis-Scott M;Harshman L;Wayne ML;Kopp A;Nuzhdin SV
通讯作者：
Nuzhdin SV
影响因子：
3.5
作者：
Kelemen O;Convertini P;Zhang Z;Wen Y;Shen M;Falaleeva M;Stamm S
通讯作者：
Stamm S
影响因子：
64.8
作者：
通讯作者：
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