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PIANA: protein interactions and network analysis. GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. CellDesigner: a process diagram editor for gene-regulatory and biochemical networks. VisANT: data-integrating visual framework for biological networks and modules. Human protein reference database-2006 update. An architecture for biological information extraction and representation. Text-mining and information-retrieval services for molecular biology. Genome-wide mapping of in vivo protein–DNA interactions. Johnson, D.S., Mortazavi, A., Myers, R.M. Human protein reference database as a discovery resource for proteomics. IntAct: an open source molecular interaction database. ArrayExpress-a public database of microarray experiments and gene expression profiles. Gene expression omnibus: microarray data storage, submission, retrieval, and analysis. CABIN: collective analysis of biological interaction networks. Estimating and improving protein interaction error rates. How reliable are experimental protein–protein interaction data? J. Weighing our measures of gene expression. GoMiner: a resource for biological interpretation of genomic and proteomic data. BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. MAPPFinder: using gene ontology and GenMAPP to create a global gene-expression profile from microarray data. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Functional genomics and proteomics: charting a multidimensional map of the yeast cell. Global studies of cell type-specific gene expression in plants. Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. Finally, we describe an application of BioNetwork Bench to the assembly and iterative expansion of a gene network that controls the differentiation of retinal progenitor cells into rod photoreceptors.Kislinger, T. It enables biologists to analyze public as well as private gene expression interactively query gene expression datasets integrate data from multiple networks store and selectively share the data and results.

CITE CYTOSCAPE SOFTWARE

We describe BioNetwork Bench, an open source, user-friendly suite of database and software tools for constructing, querying, and analyzing gene and protein network models. Although many tools and databases are currently available for accessing such data, they are left unutilized by bench scientists as they generally lack features for effective analysis and integration of both public and private datasets and do not offer an intuitive interface for use by scientists with limited computational expertise. Abstract: Gene and protein networks offer a powerful approach for integration of the disparate yet complimentary types of data that result from highthroughput analyses.

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