The analysis of patterns of gene expression patterns analysis plays an important role in developmental biology and
molecular genetics. Visualizing both quantitative and spatio-temporal aspects of gene expression patterns together with
referenced anatomical structures of a model-organism in 3D can help identifying how a group of genes are expressed at a
certain location at a particular developmental stage of an organism. In this paper, we present an approach to provide an
online visualization of gene expression data in zebrafish (Danio rerio) within 3D reconstruction model of zebrafish in
different developmental stages. We developed web services that provide programmable access to the 3D reconstruction
data and spatial-temporal gene expression data maintained in our local repositories. To demonstrate this work, we
develop a web application that uses these web services to retrieve data from our local information systems. The web
application also retrieve relevant analysis of microarray gene expression data from an external community resource; i.e.
the ArrayExpress Atlas. All the relevant gene expression patterns data are subsequently integrated with the
reconstruction data of the zebrafish atlas using ontology based mapping. The resulting visualization provides quantitative
and spatial information on patterns of gene expression in a 3D graphical representation of the zebrafish atlas in a certain
developmental stage. To deliver the visualization to the user, we developed a Java based 3D viewer client that can be
integrated in a web interface allowing the user to visualize the integrated information over the Internet.