title: The UCSC Interaction Browser: multidimensional data views in pathway context.
abstract: High-throughput data sets such as genome-wide protein-protein interactions, protein-DNA interactions and gene expression data have been published for several model systems, especially for human cancer samples. The University of California, Santa Cruz (UCSC) Interaction Browser (http://sysbio.soe.ucsc.edu/nets) is an online tool for biologists to view high-throughput data sets simultaneously for the analysis of functional relationships between biological entities. Users can access several public interaction networks and functional genomics data sets through the portal as well as upload their own networks and data sets for analysis. Users can navigate through correlative relationships for focused sets of genes belonging to biological pathways using a standard web browser. Using a new visual modality called the CircleMap, multiple 'omics' data sets can be viewed simultaneously within the context of curated, predicted, directed and undirected regulatory interactions. The Interaction Browser provides an integrative viewing of biological networks based on the consensus of many observations about genes and their products, which may provide new insights about normal and disease processes not obvious from any isolated data set.
authors.affiliation: Biomolecular Engineering Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
authors.forename: Christopher K
authors.initials: CK
authors.lastname: Wong
authors.forename: Charles J
authors.initials: CJ
authors.lastname: Vaske
authors.forename: Sam
authors.initials: S
authors.lastname: Ng
authors.forename: J Zachary
authors.initials: JZ
authors.lastname: Sanborn
authors.forename: Stephen C
authors.initials: SC
authors.lastname: Benz
authors.forename: David
authors.initials: D
authors.lastname: Haussler
authors.forename: Joshua M
authors.initials: JM
authors.lastname: Stuart
mesh_terms: D015179:Colorectal Neoplasms / Q000235:genetics; D003196:Computer Graphics; D056915:DNA Copy Number Variations; D019175:DNA Methylation; D015870:Gene Expression; D053263:Gene Regulatory Networks; D023281:Genomics; D006801:Humans; D020407:Internet; D009154:Mutation; D025941:Protein Interaction Mapping; D012984:Software