EPIC-DB: a proteomics database for studying Apicomplexan organisms.
EPIC-DB: a proteomics database for studying Apicomplexan organisms.
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DOI：
10.1186/1471-2164-10-38
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发表时间：
2009-01-21
期刊：
影响因子：
4.4
通讯作者：
Fiser A
中科院分区：
文献类型：
--
作者：
Madrid-Aliste CJ;Dybas JM;Angeletti RH;Weiss LM;Kim K;Simon I;Fiser A
高通量蛋白质组学实验可用于分析生物体的蛋白质表达，鉴定基因组的正确基因结构，或定位蛋白质内可能的翻译后修饰。高通量方法需要公开访问和易于查询的数据库，以有效地和逻辑地存储，显示和分析大量数据。EPICDB是一个可公开访问、可查询的关系数据库，它组织和显示弓形虫和微小隐孢子虫的实验性、高通量蛋白质组学数据。沿着质谱实验的详细信息，该数据库还提供抗体实验结果和功能注释分析、比较基因组学以及比对的表达序列标签（EST）和基因组开放阅读框架（ORF）序列。该数据库包含每种生物体的所有可用的替代基因数据集，其中包括相应生物体的完整理论蛋白质组，并且所有数据都引用这些序列。该数据库是围绕蛋白质序列簇构建的，这允许评估冗余、蛋白质预测差异和可能的剪接变体。该数据库可以扩展到包括其他生物体的基因组，其中蛋白质组范围的实验数据是可用的。EPICDB是一个全基因组T. gondii和C. Parvum蛋白质组学数据，并结合了许多功能，允许分析整个蛋白质组和/或注释特定的蛋白质序列。EPICDB通过提供对所有可用蛋白质序列的全面集合的完整质谱分析来补充这些生物体的其他基因组学数据库。
High throughput proteomics experiments are useful for analyzing the protein expression of an organism, identifying the correct gene structure of a genome, or locating possible post-translational modifications within proteins. High throughput methods necessitate publicly accessible and easily queried databases for efficiently and logically storing, displaying, and analyzing the large volume of data. EPICDB is a publicly accessible, queryable, relational database that organizes and displays experimental, high throughput proteomics data for Toxoplasma gondii and Cryptosporidium parvum. Along with detailed information on mass spectrometry experiments, the database also provides antibody experimental results and analysis of functional annotations, comparative genomics, and aligned expressed sequence tag (EST) and genomic open reading frame (ORF) sequences. The database contains all available alternative gene datasets for each organism, which comprises a complete theoretical proteome for the respective organism, and all data is referenced to these sequences. The database is structured around clusters of protein sequences, which allows for the evaluation of redundancy, protein prediction discrepancies, and possible splice variants. The database can be expanded to include genomes of other organisms for which proteome-wide experimental data are available. EPICDB is a comprehensive database of genome-wide T. gondii and C. parvum proteomics data and incorporates many features that allow for the analysis of the entire proteomes and/or annotation of specific protein sequences. EPICDB is complementary to other -genomics- databases of these organisms by offering complete mass spectrometry analysis on a comprehensive set of all available protein sequences.
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影响因子：
7
作者：
Zhou, XW;Blackman, MJ;Carruthers, VB
通讯作者：
Carruthers, VB
Pfam：氏族、网络工具和服务。
影响因子：
14.9
作者：
Finn, Robert D.;Mistry, Jaina;Schuster-Bockler, Benjamin;Griffiths-Jones, Sam;Hollich, Volker;Lassmann, Timo;Moxon, Simon;Marshall, Mhairi;Khanna, Ajay;Durbin, Richard;Eddy, Sean R.;Sonnhammer, Erik L. L.;Bateman, Alex
通讯作者：
Bateman, Alex
影响因子：
46.9
作者：
Washburn, MP;Wolters, D;Yates, JR
通讯作者：
Yates, JR
影响因子：
4.8
作者：
Bradley, PJ;Ward, C;Boothroyd, JC
通讯作者：
Boothroyd, JC
影响因子：
5
作者：
Jones, JL;Kruszon-Moran, D;McAuley, JB
通讯作者：
McAuley, JB