Yang Jian, Chen Lihong, Wang Lingling, Zhang Wenliang, Liu Tao, Jin Qi
State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100176, China.
BMC Genomics. 2007 Jul 25;8:250. doi: 10.1186/1471-2164-8-250.
Trichophyton rubrum is the most common dermatophyte species and the most frequent cause of fungal skin infections in humans worldwide. It's a major concern because feet and nail infections caused by this organism is extremely difficult to cure. A large set of expression data including expressed sequence tags (ESTs) and transcriptional profiles of this important fungal pathogen are now available. Careful analysis of these data can give valuable information about potential virulence factors, antigens and novel metabolic pathways. We intend to create an integrated database TrED to facilitate the study of dermatophytes, and enhance the development of effective diagnostic and treatment strategies.
All publicly available ESTs and expression profiles of T. rubrum during conidial germination in time-course experiments and challenged with antifungal agents are deposited in the database. In addition, comparative genomics hybridization results of 22 dermatophytic fungi strains from three genera, Trichophyton, Microsporum and Epidermophyton, are also included. ESTs are clustered and assembled to elongate the sequence length and abate redundancy. TrED provides functional analysis based on GenBank, Pfam, and KOG databases, along with KEGG pathway and GO vocabulary. It is integrated with a suite of custom web-based tools that facilitate querying and retrieving various EST properties, visualization and comparison of transcriptional profiles, and sequence-similarity searching by BLAST.
TrED is built upon a relational database, with a web interface offering analytic functions, to provide integrated access to various expression data of T. rubrum and comparative results of dermatophytes. It is devoted to be a comprehensive resource and platform to assist functional genomic studies in dermatophytes. TrED is available from URL: http://www.mgc.ac.cn/TrED/.
红色毛癣菌是最常见的皮肤癣菌种类，也是全球人类真菌性皮肤感染最常见的病因。这是一个主要问题，因为由这种微生物引起的足部和指甲感染极难治愈。现在已有大量包括该重要真菌病原体的表达序列标签（EST）和转录谱在内的表达数据。对这些数据进行仔细分析可以提供有关潜在毒力因子、抗原和新代谢途径的有价值信息。我们打算创建一个综合数据库TrED，以促进对皮肤癣菌的研究，并加强有效诊断和治疗策略的开发。
在时程实验中分生孢子萌发期间以及用抗真菌剂处理时红色毛癣菌的所有公开可用的EST和表达谱都存于该数据库中。此外，还包括来自毛癣菌属、小孢子菌属和表皮癣菌属三个属的22种皮肤癣菌菌株的比较基因组杂交结果。EST被聚类和组装以延长序列长度并减少冗余。TrED基于GenBank、Pfam和KOG数据库提供功能分析，以及KEGG途径和GO词汇。它与一套基于网络的定制工具集成在一起，这些工具便于查询和检索各种EST特性、转录谱的可视化和比较以及通过BLAST进行序列相似性搜索。
TrED建立在关系数据库之上，具有提供分析功能的网络界面，以提供对红色毛癣菌各种表达数据和皮肤癣菌比较结果的综合访问。它致力于成为协助皮肤癣菌功能基因组研究的全面资源和平台。可通过以下网址访问TrED：http://www.mgc.ac.cn/TrED/ 。
