SAMMD:: Staphylococcus aureus microarray meta-database
SAMMD:: Staphylococcus aureus microarray meta-database
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DOI：
10.1186/1471-2164-8-351
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发表时间：
2007-10-02
期刊：
影响因子：
4.4
通讯作者：
Elasri, Mohamed O.
中科院分区：
文献类型：
--
作者：
Nagarajan, Vijayaraj;Elasri, Mohamed O.
背景资料：金黄色葡萄球菌是一种重要的人类病原体，引起从浅表皮肤感染到严重危及生命的感染的各种疾病。S.金黄色葡萄球菌是医院感染的主要原因之一。它抵抗多种抗生素的能力构成了日益严重的公共卫生问题。为了解S.金黄色葡萄球菌，已经开发了几个全球表达谱。这些转录谱包括S.金黄色葡萄球菌和野生型在不同生长条件下的生长。这些配置文件的丰富性产生了大量的数据，但没有统一的注释系统来全面检查它们。我们报告了金黄色葡萄球菌微阵列元数据库（SAMMD）的发展，其中包括所有已发表的转录谱的数据。SAMMD是一个可通过网络访问的数据库，可帮助用户对现有的转录谱进行各种分析。描述：SAMMD是一个关系型数据库，使用MySQL作为后端，PHP/ JavaScript/DHTML作为前端。该数据库是规范化的，由五个表组成，其中包含有关基因注释，调节基因列表，实验细节，参考文献和其他细节的信息。SAMMD数据收集自同行评审的已发表文章。数据提取和转换是使用Perl脚本完成的，而数据输入是通过phpMyAdmin工具完成的。该数据库可通过网络界面访问，该界面包含几个功能，例如通过ORF ID、基因名称、基因产物名称进行简单搜索，使用基因列表进行高级搜索，在数据集之间进行比较，浏览，下载，统计和帮助。该数据库根据通用公共许可证（GPL）进行许可。结论：SAMMD托管并可在http://www.bioinformatics.org/sammd/上获得。目前有超过9500个条目的调控基因，从67个微阵列实验。SAMMD将帮助葡萄球菌科学家分析他们的表达数据，并在全球范围内了解它。它还将允许科学家将他们的转录组与其他已发表的转录组进行比较和对比。
Background: Staphylococcus aureus is an important human pathogen, causing a wide variety of diseases ranging from superficial skin infections to severe life threatening infections. S. aureus is one of the leading causes of nosocomial infections. Its ability to resist multiple antibiotics poses a growing public health problem. In order to understand the mechanism of pathogenesis of S. aureus, several global expression profiles have been developed. These transcriptional profiles included regulatory mutants of S. aureus and growth of wild type under different growth conditions. The abundance of these profiles has generated a large amount of data without a uniform annotation system to comprehensively examine them. We report the development of the Staphylococcus aureus Microarray meta-database (SAMMD) which includes data from all the published transcriptional profiles. SAMMD is a web-accessible database that helps users to perform a variety of analysis against and within the existing transcriptional profiles.Description: SAMMD is a relational database that uses MySQL as the back end and PHP/ JavaScript/DHTML as the front end. The database is normalized and consists of five tables, which holds information about gene annotations, regulated gene lists, experimental details, references, and other details. SAMMD data is collected from the peer-reviewed published articles. Data extraction and conversion was done using perl scripts while data entry was done through phpMyAdmin tool. The database is accessible via a web interface that contains several features such as a simple search by ORF ID, gene name, gene product name, advanced search using gene lists, comparing among datasets, browsing, downloading, statistics, and help. The database is licensed under General Public License ( GPL).Conclusion: SAMMD is hosted and available at http://www.bioinformatics.org/sammd/. Currently there are over 9500 entries for regulated genes, from 67 microarray experiments. SAMMD will help staphylococcal scientists to analyze their expression data and understand it at global level. It will also allow scientists to compare and contrast their transcriptome to that of the other published transcriptomes.