AnaLysis of Expression on human chromosome 21, ALE-HSA21: a pilot integrated web resource.
AnaLysis of Expression on human chromosome 21, ALE-HSA21: a pilot integrated web resource.
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DOI：
10.1093/database/bau009
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发表时间：
2014
期刊：
影响因子：
--
通讯作者：
Costa V
中科院分区：
文献类型：
--
作者：
Scarpato M;Esposito R;Evangelista D;Aprile M;Ambrosio MR;Angelini C;Ciccodicola A;Costa V
转录组研究表明，转录的普遍性，证明几乎所有的基因进行选择性剪接。准确地注释基因的所有转录本是至关重要的。需要了解突变对表型的影响，阐明mRNA的遗传和表观遗传调控，更广泛地扩大我们对细胞功能和组织多样性的了解。RNA测序（RNA-Seq）和下一代测序的其他应用提供了宝贵的数据来提高注释的准确性，同时产生了与所产生数据的多样性、复杂性和大小相关的问题。在这种“场景”中，由于缺乏易于用户使用的资源，生物信息学技能较低的研究人员很容易获得这些资源，因此在不浏览大量数据库的情况下很难检索有关一个或几个基因的完整信息。一致地，越来越多的数据从“组学”技术迫使开发集成数据库合并不同的数据格式来自不同的，但互补的来源。鉴于这些考虑，并且考虑到对研究唐氏综合征（一种由于人类21号染色体三体（HSA 21）引起的遗传疾病）的广泛兴趣，我们开发了一个集成的关系数据库和一个网络界面，名为ALE-HSA 21（HSA 21上的表达分析），可在http://bioinfo.na.iac.cnr.it/ALE-HSA21上访问。这个全面和用户友好的网络资源整合了所有编码和非编码的21号染色体转录本-现有的基因注释和转录本确定从头通过RNA-Seq分析与预测计算分析的调控序列。考虑到非编码RNA和编码基因的非翻译区在关键调控机制中的作用，ALE-HSA 21也是一个有趣的基于网络的平台来研究这些过程。ALE-HSA 21的“以转录物为中心”和易于获得的性质使得该资源成为在亚型水平而不是在基因水平快速检索数据的有价值的工具，可用于研究涉及21号染色体基因的任何疾病、分子途径或细胞过程。数据库URL：http://bioinfo.na.iac.cnr.it/ALE-HSA21/
Transcriptome studies have shown the pervasive nature of transcription, demonstrating almost all the genes undergo alternative splicing. Accurately annotating all transcripts of a gene is crucial. It is needed to understand the impact of mutations on phenotypes, to shed light on genetic and epigenetic regulation of mRNAs and more generally to widen our knowledge about cell functionality and tissue diversity. RNA-sequencing (RNA-Seq), and the other applications of the next-generation sequencing, provides precious data to improve annotations' accuracy, simultaneously creating issues related to the variety, complexity and the size of produced data. In this ‘scenario’, the lack of user-friendly resources, easily accessible to researchers with low skills in bioinformatics, makes difficult to retrieve complete information about one or few genes without browsing a jungle of databases. Concordantly, the increasing amount of data from ‘omics’ technologies imposes to develop integrated databases merging different data formats coming from distinct but complementary sources. In light of these considerations, and given the wide interest in studying Down syndrome—a genetic condition due to the trisomy of human chromosome 21 (HSA21)—we developed an integrated relational database and a web interface, named ALE-HSA21 (AnaLysis of Expression on HSA21), accessible at http://bioinfo.na.iac.cnr.it/ALE-HSA21. This comprehensive and user-friendly web resource integrates—for all coding and noncoding transcripts of chromosome 21—existing gene annotations and transcripts identified de novo through RNA-Seq analysis with predictive computational analysis of regulatory sequences. Given the role of noncoding RNAs and untranslated regions of coding genes in key regulatory mechanisms, ALE-HSA21 is also an interesting web-based platform to investigate such processes. The ‘transcript-centric’ and easily-accessible nature of ALE-HSA21 makes this resource a valuable tool to rapidly retrieve data at the isoform level, rather than at gene level, useful to investigate any disease, molecular pathway or cell process involving chromosome 21 genes. Database URL: http://bioinfo.na.iac.cnr.it/ALE-HSA21/
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影响因子：
7
作者：
Harrow J;Frankish A;Gonzalez JM;Tapanari E;Diekhans M;Kokocinski F;Aken BL;Barrell D;Zadissa A;Searle S;Barnes I;Bignell A;Boychenko V;Hunt T;Kay M;Mukherjee G;Rajan J;Despacio-Reyes G;Saunders G;Steward C;Harte R;Lin M;Howald C;Tanzer A;Derrien T;Chrast J;Walters N;Balasubramanian S;Pei B;Tress M;Rodriguez JM;Ezkurdia I;van Baren J;Brent M;Haussler D;Kellis M;Valencia A;Reymond A;Gerstein M;Guigó R;Hubbard TJ
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Hubbard TJ
在致癌 BRAF 诱导的黑色素瘤小鼠模型中体内鉴定肿瘤抑制性 PTEN ceRNA。
影响因子：
64.5
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Karreth FA;Tay Y;Perna D;Ala U;Tan SM;Rust AG;DeNicola G;Webster KA;Weiss D;Perez-Mancera PA;Krauthammer M;Halaban R;Provero P;Adams DJ;Tuveson DA;Pandolfi PP
通讯作者：
Pandolfi PP
影响因子：
3.7
作者：
Costa V;Esposito R;Aprile M;Ciccodicola A
通讯作者：
Ciccodicola A
影响因子：
56.9
作者：
Kapranov, Philipp;Cheng, Jill;Gingeras, Thomas R.
通讯作者：
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通过未翻译基因区域和其他非编码元件调节真核基因表达。
影响因子：
8
作者：
Barrett, Lucy W.;Fletcher, Sue;Wilton, Steve D.
通讯作者：
Wilton, Steve D.