Thursday, September 23, 2010

GRANITE- Gene RelAtional Network of InTeracting Elements

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This is the tool that is generated by me as a part of center of biomedical informatics (CBMI) at Washington University School of Medicine. The advent of new profiling technologies has enabled the comprehensive study of complex multi-factorial diseases such as cancers. The end product of such experiments is often a set of genes that are of interest to the researchers. Gene Relational Networks (GRNs) offer a possible means of establishing functional relationship among these genes. Although many tools to generate GRNs exist, they depend only on certain types of databases to infer relations among genes, preventing the user from having comprehensive interaction information. To address this issue, we developed a novel application termed GRANITE. GRANITE employs a unique workflow based on prioritization of databases to construct GRNs. Unlike some of the current available tools that employ one or two types of databases, GRANITE is comprehensive in the types of databases that it uses. A web application employing a Cytoscape plugin allows researchers to construct GRNs by entering a set of genes of interest and by selecting one or more databases from which connections are determined. A caBIG®-compatible stateful analytical service is also built for GRANITE using Introduce toolkit. GRANITE is publicly available through a web-based user interface, which guides users through the construction and visualization of GRNs (http://bioinformatics.wustl.edu/webTools/HomeAction.do). A user manual illustrating different features is also available at http://cvswiki1.wustl.edu/nagarajanwiki/GRANITE?action=AttachFile&do=view&target=GRANITEuserManual1.pdf. GRANITE is also programmatically accessible through a caBIG® compliant analytical service. The GRANITE analytical service is available at (http://analysis1.wustl.edu/wsrf/services/cagrid/GRANITE). The client code for this analytical service is available at http://cvswiki1.wustl.edu/nagarajanwiki/GRANITE?action=AttachFile&do=get&target=GRANITEregNminClient.zip . The user manual that provides instructions to run the client code are available at http://cvswiki1.wustl.edu/nagarajanwiki/GRANITE?action=AttachFile&do=get&target=UserManual.docx .

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