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3D Visual Integration of Spatio-Temporal Gene Expression Patterns on Digital Atlas of Zebrafish Embryo using Web Service
International Journal on Information Technology, 1 (3): 7 (декабря 2011)
Аннотация
Gene expression patterns analysis with microarray
provides quantitative information that shows how a gene is
expressed under a particular condition. Whole mount in situ
hybridization, on the other hand, can be used to capture the
spatio-temporal characteristics of the gene expression pattern.
Therefore, visual integration of gene expression data from
both techniques with a digital atlas data of a model-organism
can help identifying not only spatial and temporal but also
quantitative aspects of gene expression in different stages of
development. In this paper, we present an approach using web
services to provide an integrative online visualization of gene
expression patterns in within a digital atlas of zebrafish in
different stages of development. We developed SOAP web
services that provide programmatic access to the 3D data and
spatial-temporal whole mount gene expression data to our
readily developed information systems; the 3D digital atlas of
zebrafish development and the Gene Expression Management
System (GEMS). We also created web applications that exploit
the newly developed web services to retrieve data from our
repositories. The web applications also uses the web services
to retrieve relevant quantitative microarray analysis gene
expression data from community resources; i.e. the
ArrayExpress Atlas. All the gene expression patterns data and
the 3D atlas data are subsequently integrated using ontology
based mapping. In order to deliver the integrated visualization
to end users, we developed a Java based 3D-viewer client that
can be integrated in a web interface allowing users to visualize
the information over Internet.
