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TrED: the Trichophyton rubrum Expression Database
Jian Yang1, Lihong Chen, Lingling Wang
1State 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. yang@chgb.org.cn
Background:
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.
Description:
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.
Conclusion:
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/.
Insights
Trichophyton rubrum causes difficult-to-treat fungal infections. The Trichophyton database (TrED) integrates gene expression data to aid in understanding virulence and developing new treatments for dermatophytes.
Area of Science:
- Mycology
- Genomics
- Bioinformatics
Background:
- Trichophyton rubrum is a prevalent dermatophyte causing persistent fungal skin and nail infections.
- Understanding T. rubrum's genetic and metabolic pathways is crucial for developing effective treatments.
- Existing expression data offers insights into virulence factors and antigens.
Purpose of the Study:
- To create an integrated database, TrED, for dermatophyte functional genomics.
- To facilitate the study of T. rubrum and related fungi.
- To enhance the development of diagnostic and treatment strategies for fungal infections.
Main Methods:
- Integrated publicly available expressed sequence tags (ESTs) and transcriptional profiles of T. rubrum.
- Included comparative genomics hybridization results for 22 dermatophyte strains.
- Developed web-based tools for data querying, visualization, and sequence similarity searching using BLAST.
Main Results:
- Assembled and clustered ESTs to improve sequence length and reduce redundancy.
- Performed functional analysis using GenBank, Pfam, KOG, KEGG, and GO databases.
- Provided integrated access to T. rubrum expression data and comparative dermatophyte results.
Conclusions:
- TrED offers a comprehensive resource for dermatophyte functional genomics research.
- The database facilitates integrated access to diverse expression data and comparative analyses.
- TrED serves as a valuable platform for advancing the study of fungal pathogens.
