Zebrafish as a model system
In addition to its rapid and extern development, the zebrafish, a fresh water fish originally from India is a popular model system for developmental and genetic studies.
A direct result of the advantageous that this species has, a huge amount of data has been produced as genomic, proteomic, behavioral as well as images.
Gene Expression Managment System (GEMS)
This resource contains 3D patterns of gene expression during zebrafish development. The visualization of the gene expression is accomplished through In Situ hybridization (ISH) and based on an ISH protocol specifically developed for zebrafish: zebraFISH (Welten et al, 2006). Images of these 3D patterns are acquired using Confocal Laser Scanner Microscopy (CLSM). The 3D images are annotated with formal ontologies i.e. the Gene Ontology (GO) and the Developmental Anatomy Ontology of Zebrafish (DAOZ) and are stored in the GEMS; a Java-based application. GEMS could be considered as a content management system where the content in this case is the 3D patterns of gene expression and there annotations, experimental conditions (cf. zebraFISH protocol) as well as imaging conditions.
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News
- To increase comparative studies and analysis of gene expression patterns, we developed mining tools. These tool have been integrated within GEMS. We applied association rules techniques to uncover possible relations between genes. Association patterns are extracted from the GEMS database and are directly integrated with each other for a primary comparison. The uniform annotation of the gene expression data with formal ontologies enables cross-reference with other resources. This situation permits advanced comparisons and evaluations of the discovered patterns. The mined association patterns are still under review and will be released soon...
- Now in GEMS: expression patterns of 14-3-3 proteins. These patterns will be published soon...
Last modified: November 2010.