Nagarajan Vijayaraj, Elasri Mohamed O
Department of Biological Sciences; The University of Southern Mississippi, MS, 39406, USA.
BMC Genomics. 2007 Oct 2;8:351. doi: 10.1186/1471-2164-8-351.
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.
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).
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.
金黄色葡萄球菌是一种重要的人类病原体，可引发从浅表皮肤感染到严重威胁生命的感染等多种疾病。金黄色葡萄球菌是医院感染的主要原因之一。其对多种抗生素的耐药能力给公共卫生带来了日益严重的问题。为了了解金黄色葡萄球菌的致病机制，已开发了几种全局表达谱。这些转录谱包括金黄色葡萄球菌的调控突变体以及野生型在不同生长条件下的生长情况。这些谱的丰富性产生了大量数据，但却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）的开发情况，该数据库包含了所有已发表转录谱的数据。SAMMD是一个可通过网络访问的数据库，可帮助用户针对现有转录谱进行各种分析，并在这些转录谱内部进行分析。
SAMMD是一个关系数据库，以MySQL作为后端，以PHP/JavaScript/DHTML作为前端。该数据库经过规范化处理，由五个表组成，这些表保存有关基因注释、调控基因列表、实验细节、参考文献和其他细节的信息。SAMMD数据是从经过同行评审发表的文章中收集的。数据提取和转换使用perl脚本完成，而数据录入则通过phpMyAdmin工具进行。该数据库可通过一个网络界面访问，该界面具有多种功能，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）授权。
SAMMD托管于http://www.bioinformatics.org/sammd/ 并可供使用。目前有来自67个微阵列实验的超过9500个调控基因条目。SAMMD将帮助葡萄球菌科学家分析他们的表达数据，并在全局层面理解这些数据。它还将使科学家能够将他们的转录组与其他已发表的转录组进行比较和对比。
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