Welcome to the e-Fungi data warehouse

e-Fungi is a joint research project between the School of Computer Science and the Faculty of Life Sciences at the University of Manchester and the Departments of Computer Science and Biological Sciences at the University of Exeter

The data warehouse that is being developed as part of the e-Fungi project and that can be accessed here integrates sequence data from multiple fungal sequences in a way that facilitates the systematic comparative study of those genomes. Less well understood species can be studied with reference to model organisms with more fully explored functional characteristics.

To support comparative functional genomics we provide a library of bioinformatics queries and analyses that make use of the warehouse, and which can be combined in different ways to conduct studies of pathogenicity and evolution.

The warehouse contains genomic data, EST data, Gene Ontology annotation, KEGG pathways and results of the following analyses performed over the genomic data:

• MCL
• OrthoMCL
• PSORT II prediction of protein localisation sites in cells
• WoLF PSORT prediction or protein localisation
• SignalP prediction of secreted proteins
• Pfam domain identification

The warehouse currently contains genomic data of the following 34 fungal genomes and 2 oomycetes:

genome	taxonomy	pathogenicity	growth form
Aspergillus fumigatus	Ascomycete - Eurotiomycetes	animal pathogen	filamentous
Aspergillus nidulans	Ascomycete - Eurotiomycetes	non pathogen	filamentous
Aspergillus niger	Ascomycete - Eurotiomycetes	non pathogen	filamentous
Aspergillus oryzae	Ascomycete - Eurotiomycetes	non pathogen	filamentous
Aspergillus terreus	Ascomycete - Eurotiomycetes	animal pathogen	filamentous
Botrytis cinerea	Ascomycete - Leotiomycetes	plant pathogen	filamentous
Candida albicans	Ascomycete - Saccharomycetes	animal pathogen	psuedo hyphae - dimorphic
Candida glabrata	Ascomycete - Saccharomycetes	animal pathogen	psuedo hyphae - dimorphic
Candida lusitaniae	Ascomycete - Saccharomycetes	animal pathogen	yeast - dimorphic
Chaetomium globosum	Ascomycete - Sordariomycetes	animal pathogen	filamentous
Coccidioides immitis	Ascomycete - Eurotiomycetes	animal pathogen	filamentous
Debaryomyces hansenii	Ascomycete - Saccharomycetes	non pathogen	yeast - dimorphic
Encephalitozoon cuniculi	Microsporidia	animal pathogen	microsporidia
Eremothecium gossypii	Ascomycete - Saccharomycetes	plant pathogen	yeast - dimorphic
Gibberella zeae	Ascomycete - Sordariomycetes	plant pathogen	filamentous
Kluyveromyces lactis	Ascomycete - Saccharomycetes	non pathogen	yeast
Kluyveromyces waltii	Ascomycete - Saccharomycetes	non pathogen	yeast
Magnaporthe grisea	Ascomycete - Sordariomycetes	plant pathogen	filamentous
Neurospora crassa	Ascomycete - Sordariomycetes	non pathogen	filamentous
Phanerochaete chrysosporium	Basidiomycete - Homobasidiomycota	non pathogen	filamentous
Phytophthora ramorum	Oomycete	plant pathogen	filamentous
Phytophthora sojae	Oomycete	plant pathogen	filamentous
Rhizopus oryzae	Zygomycota - Mucorales	animal pathogen	filamentous
Saccharomyces bayanus	Ascomycete - Saccharomycetes	non pathogen	yeast
Saccharomyces castellii	Ascomycete - Saccharomycetes	non pathogen	yeast
Saccharomyces cerevisiae	Ascomycete - Saccharomycetes	non pathogen	yeast
Saccharomyces kluyveri	Ascomycete - Saccharomycetes	non pathogen	yeast
Saccharomyces kudriavzevii	Ascomycete - Saccharomycetes	non pathogen	yeast
Saccharomyces mikatae	Ascomycete - Saccharomycetes	non pathogen	yeast
Saccharomyces paradoxus	Ascomycete - Saccharomycetes	non pathogen	yeast
Schizosaccharomyces pombe	Ascomycete - Schizosaccharomycetes	non pathogen	yeast - fission
Sclerotinia sclerotiorum	Ascomycete - Leotiomycetes	plant pathogen	filamentous
Stagonospora nodorum	Ascomycete - Dothideomycetes	plant pathogen	filamentous
Trichoderma reesei	Ascomycete - Sordariomycetes	non pathogen	filamentous
Ustilago maydis	Basidiomycete - Ustilaginomycota	plant pathogen	filamentous
Yarrowia lipolytica	Ascomycete - Saccharomycetes	non pathogen	yeast - dimorphic

The warehouse also contains EST data of the following genomes:

• Aspergillus nidulans
• Gibberella zeae
• Magnaporthe grisea
• Phanerochaete chrysosporium
• Phytophthora sojae
• Saccharomyces cerevisiae
• Schizosaccharomyces pombe
• Trichoderma reesei
• Ustilago maydis

The data in the warehouse can be accessed using either of the following methods:

• Browse: provides an entry point to the database allowing the user to browse and explore the data by following the links provided.
• Simple Search: provides access to the analysis library.
• Advanced Search: enables the filtering of data.

For further information on each of those access methods please refer to the documentation, which provides more detailed introduction of how to access the database. A list of all the queries currently provided can be found in the documentation of the Simple Search.

For the majority of simple searches, web services are also provided. The WSDL can be found here: WSDL. For documentation of the web services, please refer to the documentation of the simple searches.

The next database release is planned for the end of 2007.