APASdb: a database describing alternative poly(A) sites and selection of heterogeneous cleavage sites downstream of poly(A) signals.
APASdb: a database describing alternative poly(A) sites and selection of heterogeneous cleavage sites downstream of poly(A) signals.
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DOI：
10.1093/nar/gku1076
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发表时间：
2015-01
影响因子：
14.9
通讯作者：
Xu A
中科院分区：
文献类型：
--
作者：
You L;Wu J;Feng Y;Fu Y;Guo Y;Long L;Zhang H;Luan Y;Tian P;Chen L;Huang G;Huang S;Li Y;Li J;Chen C;Zhang Y;Chen S;Xu A
越来越多的基因被证明根据细胞和组织的类型和/或加工时的生理和病理条件而利用替代的多聚腺苷化(APA)3‘-加工位点，而关于APA的全基因组数据库的构建是为了更好地理解特定生物的PolyA(A)位点选择和APA指导的基因表达调控。在这里，我们提供了一个可在网络上访问的数据库，名为APASDB(http://mosas.sysu.edu.cn/utr)，)，它可以可视化所有基因不同APA亚型的精确图谱和使用量化。数据集通过高通量测序多聚腺苷酸化转录本的3‘端的SAPAS方法进行了深入的分析。因此，APASdb详细说明了Poly(A)信号下游的所有异质切割位点，并保持了对APA位点的几乎完全覆盖，比以前使用传统方法的数据库要好得多。此外，APASdb通过计算相应的标准化读数，在不同APA位点的转录本中提供给定APA变体的量化，使我们的数据库更有用。此外，APASdb支持基于URL的检索、浏览和显示外显子-内含子结构、Poly(A)信号、Poly(A)位点位置和使用情况阅读以及3‘-非翻译区(3’-UTRs)。目前，APASdb参与了人类、小鼠和斑马鱼的各种生物学过程和疾病。
Increasing amounts of genes have been shown to utilize alternative polyadenylation (APA) 3′-processing sites depending on the cell and tissue type and/or physiological and pathological conditions at the time of processing, and the construction of genome-wide database regarding APA is urgently needed for better understanding poly(A) site selection and APA-directed gene expression regulation for a given biology. Here we present a web-accessible database, named APASdb (http://mosas.sysu.edu.cn/utr), which can visualize the precise map and usage quantification of different APA isoforms for all genes. The datasets are deeply profiled by the sequencing alternative polyadenylation sites (SAPAS) method capable of high-throughput sequencing 3′-ends of polyadenylated transcripts. Thus, APASdb details all the heterogeneous cleavage sites downstream of poly(A) signals, and maintains near complete coverage for APA sites, much better than the previous databases using conventional methods. Furthermore, APASdb provides the quantification of a given APA variant among transcripts with different APA sites by computing their corresponding normalized-reads, making our database more useful. In addition, APASdb supports URL-based retrieval, browsing and display of exon-intron structure, poly(A) signals, poly(A) sites location and usage reads, and 3′-untranslated regions (3′-UTRs). Currently, APASdb involves APA in various biological processes and diseases in human, mouse and zebrafish.
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DOI：
10.1093/database/bau076
发表时间：
2014-07-22
影响因子：
5.8
作者：
Mueller, Soeren;Rycak, Lukas;Rotter, Bjoern
通讯作者：
Rotter, Bjoern
影响因子：
12.3
作者：
Langmead B;Schatz MC;Lin J;Pop M;Salzberg SL
通讯作者：
Salzberg SL
影响因子：
14.9
作者：
Grillo G;Turi A;Licciulli F;Mignone F;Liuni S;Banfi S;Gennarino VA;Horner DS;Pavesi G;Picardi E;Pesole G
通讯作者：
Pesole G
影响因子：
14.9
作者：
Tian B;Hu J;Zhang H;Lutz CS
通讯作者：
Lutz CS
影响因子：
7
作者：
Beaudoing, E;Gautheret, D
通讯作者：
Gautheret, D