{"title":"利用web服务可视化和分析斑马鱼的三维基因表达模式","authors":"D. Potikanond, F. Verbeek","doi":"10.1117/12.909810","DOIUrl":null,"url":null,"abstract":"The analysis of patterns of gene expression patterns analysis plays an important role in developmental biology and \nmolecular genetics. Visualizing both quantitative and spatio-temporal aspects of gene expression patterns together with \nreferenced anatomical structures of a model-organism in 3D can help identifying how a group of genes are expressed at a \ncertain location at a particular developmental stage of an organism. In this paper, we present an approach to provide an \nonline visualization of gene expression data in zebrafish (Danio rerio) within 3D reconstruction model of zebrafish in \ndifferent developmental stages. We developed web services that provide programmable access to the 3D reconstruction \ndata and spatial-temporal gene expression data maintained in our local repositories. To demonstrate this work, we \ndevelop a web application that uses these web services to retrieve data from our local information systems. The web \napplication also retrieve relevant analysis of microarray gene expression data from an external community resource; i.e. \nthe ArrayExpress Atlas. All the relevant gene expression patterns data are subsequently integrated with the \nreconstruction data of the zebrafish atlas using ontology based mapping. The resulting visualization provides quantitative \nand spatial information on patterns of gene expression in a 3D graphical representation of the zebrafish atlas in a certain \ndevelopmental stage. To deliver the visualization to the user, we developed a Java based 3D viewer client that can be \nintegrated in a web interface allowing the user to visualize the integrated information over the Internet.","PeriodicalId":89305,"journal":{"name":"Visualization and data analysis","volume":"40 1","pages":"829412"},"PeriodicalIF":0.0000,"publicationDate":"2012-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"6","resultStr":"{\"title\":\"Visualization and analysis of 3D gene expression patterns in zebrafish using web services\",\"authors\":\"D. Potikanond, F. Verbeek\",\"doi\":\"10.1117/12.909810\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"The analysis of patterns of gene expression patterns analysis plays an important role in developmental biology and \\nmolecular genetics. Visualizing both quantitative and spatio-temporal aspects of gene expression patterns together with \\nreferenced anatomical structures of a model-organism in 3D can help identifying how a group of genes are expressed at a \\ncertain location at a particular developmental stage of an organism. In this paper, we present an approach to provide an \\nonline visualization of gene expression data in zebrafish (Danio rerio) within 3D reconstruction model of zebrafish in \\ndifferent developmental stages. We developed web services that provide programmable access to the 3D reconstruction \\ndata and spatial-temporal gene expression data maintained in our local repositories. To demonstrate this work, we \\ndevelop a web application that uses these web services to retrieve data from our local information systems. The web \\napplication also retrieve relevant analysis of microarray gene expression data from an external community resource; i.e. \\nthe ArrayExpress Atlas. All the relevant gene expression patterns data are subsequently integrated with the \\nreconstruction data of the zebrafish atlas using ontology based mapping. The resulting visualization provides quantitative \\nand spatial information on patterns of gene expression in a 3D graphical representation of the zebrafish atlas in a certain \\ndevelopmental stage. To deliver the visualization to the user, we developed a Java based 3D viewer client that can be \\nintegrated in a web interface allowing the user to visualize the integrated information over the Internet.\",\"PeriodicalId\":89305,\"journal\":{\"name\":\"Visualization and data analysis\",\"volume\":\"40 1\",\"pages\":\"829412\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2012-01-22\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"6\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Visualization and data analysis\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1117/12.909810\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Visualization and data analysis","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1117/12.909810","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
Visualization and analysis of 3D gene expression patterns in zebrafish using web services
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.