TrED: the <it>Trichophyton rubrum </it>Expression Database
<p>Abstract</p> <p>Background</p> <p><it>Trichophyton rubrum </it>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 org...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2007-07-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/8/250 |
| _version_ | 1818749716030029824 |
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| author | Liu Tao Zhang Wenliang Wang Lingling Chen Lihong Yang Jian Jin Qi |
| author_facet | Liu Tao Zhang Wenliang Wang Lingling Chen Lihong Yang Jian Jin Qi |
| author_sort | Liu Tao |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p><it>Trichophyton rubrum </it>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.</p> <p>Description</p> <p>All publicly available ESTs and expression profiles of <it>T. rubrum </it>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, <it>Trichophyton</it>, <it>Microsporum </it>and <it>Epidermophyton</it>, 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.</p> <p>Conclusion</p> <p>TrED is built upon a relational database, with a web interface offering analytic functions, to provide integrated access to various expression data of <it>T. rubrum </it>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: <url>http://www.mgc.ac.cn/TrED/</url>.</p> |
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| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-18T04:08:12Z |
| publishDate | 2007-07-01 |
| publisher | BMC |
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| series | BMC Genomics |
| spelling | doaj.art-4861e4f2223e450f8cabb7423a6e33a22022-12-21T21:21:32ZengBMCBMC Genomics1471-21642007-07-018125010.1186/1471-2164-8-250TrED: the <it>Trichophyton rubrum </it>Expression DatabaseLiu TaoZhang WenliangWang LinglingChen LihongYang JianJin Qi<p>Abstract</p> <p>Background</p> <p><it>Trichophyton rubrum </it>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.</p> <p>Description</p> <p>All publicly available ESTs and expression profiles of <it>T. rubrum </it>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, <it>Trichophyton</it>, <it>Microsporum </it>and <it>Epidermophyton</it>, 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.</p> <p>Conclusion</p> <p>TrED is built upon a relational database, with a web interface offering analytic functions, to provide integrated access to various expression data of <it>T. rubrum </it>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: <url>http://www.mgc.ac.cn/TrED/</url>.</p>http://www.biomedcentral.com/1471-2164/8/250 |
| spellingShingle | Liu Tao Zhang Wenliang Wang Lingling Chen Lihong Yang Jian Jin Qi TrED: the <it>Trichophyton rubrum </it>Expression Database BMC Genomics |
| title | TrED: the <it>Trichophyton rubrum </it>Expression Database |
| title_full | TrED: the <it>Trichophyton rubrum </it>Expression Database |
| title_fullStr | TrED: the <it>Trichophyton rubrum </it>Expression Database |
| title_full_unstemmed | TrED: the <it>Trichophyton rubrum </it>Expression Database |
| title_short | TrED: the <it>Trichophyton rubrum </it>Expression Database |
| title_sort | tred the it trichophyton rubrum it expression database |
| url | http://www.biomedcentral.com/1471-2164/8/250 |
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