MIMAS - Genome Bioinformatics Group

• Forschungsstelle: SIB
• Projektnummer: SIB 2001-7 MIMAS
• Projekttitel Englisch: MIMAS - Genome Bioinformatics Group

Kurzbeschreibung (Englisch)

The Microarray Information Management & Analysis System (MIMAS) is a platform dedicated to storage and analysis of microarray data. MIMAS is the basis for highly flexible data analysis both at the level of individual experiments and at the level of large-scale data mining. The former aims at idintifying particular genes important for certain processes and the latter exploits high-quality array data to test novel approaches to statistical analysis of genome biological data.

GermOnline is a cross-species prototype database that provides access to microarray expression data from experiments relevant for the mitotic and meiotic cell cycle as well as gametogenesis in yeast and higher eukaryotes. In addition to that, GermOnline integrates knowledge about genes important for sexual reproduction that is provided, curated and updated by members of the scientific community who work in the field. This novel approach to community-based knowledge curation is applicable to all conserved processes studied in a variety of model systems.

The genome of the haploid filamentous fungus Ashbya gossypii was sequenced, assembled, and fully annotated by the laboratory of Peter Philippsen in collaboration with Syngenta Inc. The vast majority of Ashbya genes are highly homologous and syntenic (their chromosomal order is conserved) to their orthologues in the budding yeast S. cerevisiae. Therefore, the Ashbya Genome Databese (AGD) will be very useful tool for the various yeast communities as well as biologists who are interested in evolutionary aspects of genome research.

DNA mocroarray technology is currently applied in four different types of experiments. First, genomic DNA is screened to identify polymorphisms and genetic rearrangements as well as gene deletions and duplications. Second, arrays are used to map origins of DNA replication. Third, gene expression profiles that underlie e.g. development, drug response, cancer and the response to host-pathogen interactions are established. Fourth, target sites recognized by DNA binding proteins are identified at a genome-wide level.

Abstract (Englisch)

Microarray Information Management & Analysis System (MIMAS)

The Genome Biology group develops the Microarray Information Management & Analysis System (MIMAS) within the framework of the Swiss Array Consortium (SAC) which is an association of research facilities that provide access to microarray technology. MIMAS is a platform for the analysis of microarray data and large-scale data mining. Array data and their cognate MIAME compliant (Minimal Information About a Microarray Experiement) meta-data will be stored in a central relational data-base to enable life scientists a highly flexible approach to data analysis at the level of individual experiments. Any set of hybridization experiments can be combined with available appropriate control data to increase the impact of the conclusions dreawn from the analysis. Scientists will be able to work with various commercially available and open source analysis tools for statistical and cluster analysis to filter genes and cluster them according to their expression patterns. Moreover, researchers in the filed of statistics will be able to develop and test novel approaches to the analysis of highly standardized biological data. Finally, MIMAS provides online access to analysis toolds developed by Eytan Domany (CTWC server at http://www.biozentrum.unibas.ch/corelab/ctwc.html) and Michel Bellis (Arrayon) within the framework of collaborations.

The GermOnline Database

GermOnline provides information and microarray expression data for genes involved in mitosis and meiosis, gamete formation and germ line development across species. The database has been developed, and is being curated and updated by life scientists in cooperation with bioinformaticists. Information is contributed through an online form using free text, images and the controlled vocabulary developed by the GeneOntology consortium. Authors provide up to three references in support of their contribution. The database is governed by an international board of scientists to ensure a standardized data format and the highest quality of GermOnline's information content. Release 2.0 provides exclusive access to microarray expression data from S. cerevisiae and R. norvegicus, as well as curated information on approximately 700 genes from various organisms. GermOnline, a fully operational prototype subject-oriented knowledge-base designed for community annotation and array data visualization, is accessible at http://www.germonline.org. The target audience includes researchers who work on the mitotic cell division, meiosis, gametogenesis, germ line development, human reproductive health and comparative genomics.

The Ashbya Genome Databse (AGD)

Ashbya gossypii is a haploid filamentous fungus that belongs to the class of Ascomycetae. Its genome contains approximately 4720 protein encoding loci, which are organized in seven chromosomes. Ashbya genes are highly homologous and syntenic (their chromosomal order is conserved) to those from budding yeast. Moreover, the Ashbya genome provides excellent evidence in support of a previously postulated genome duplication event in the yeast Saccharomyces. Therefore the AGD will be avery useful tool for the large community of yeast researchers as well a biologists who are interested in evolutionary aspects of genome research. The Ashbya genome has now been sepquenced, assembled and fully annotated by the laboratory of Peter Philippsen in collaboration with Syngenta Inc. The database model, a graphical user interface (GUI) and an appropriate three-way synteny viewer (one Ashbya chromosome versus two Saccharomyces chromosomes) are currently under development.