title: VisANT 3.0: new modules for pathway visualization, editing, prediction and construction.
abstract: With the integration of the KEGG and Predictome databases as well as two search engines for coexpressed genes/proteins using data sets obtained from the Stanford Microarray Database (SMD) and Gene Expression Omnibus (GEO) database, VisANT 3.0 supports exploratory pathway analysis, which includes multi-scale visualization of multiple pathways, editing and annotating pathways using a KEGG compatible visual notation and visualization of expression data in the context of pathways. Expression levels are represented either by color intensity or by nodes with an embedded expression profile. Multiple experiments can be navigated or animated. Known KEGG pathways can be enriched by querying either coexpressed components of known pathway members or proteins with known physical interactions. Predicted pathways for genes/proteins with unknown functions can be inferred from coexpression or physical interaction data. Pathways produced in VisANT can be saved as computer-readable XML format (VisML), graphic images or high-resolution Scalable Vector Graphics (SVG). Pathways in the format of VisML can be securely shared within an interested group or published online using a simple Web link. VisANT is freely available at http://visant.bu.edu.
authors.affiliation: Center for Advanced Genomic Technology, Boston University, Boston, MA 02215, USA.
authors.forename: Zhenjun
authors.initials: Z
authors.lastname: Hu
authors.forename: David M
authors.initials: DM
authors.lastname: Ng
authors.forename: Takuji
authors.initials: T
authors.lastname: Yamada
authors.forename: Chunnuan
authors.initials: C
authors.lastname: Chen
authors.forename: Shuichi
authors.initials: S
authors.lastname: Kawashima
authors.forename: Joe
authors.initials: J
authors.lastname: Mellor
authors.forename: Bolan
authors.initials: B
authors.lastname: Linghu
authors.forename: Minoru
authors.initials: M
authors.lastname: Kanehisa
authors.forename: Joshua M
authors.initials: JM
authors.lastname: Stuart
authors.forename: Charles
authors.initials: C
authors.lastname: DeLisi
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics / Q000639:trends*; D003628:Database Management Systems / Q000706:statistics & numerical data; D030541:Databases, Genetic / Q000706:statistics & numerical data; D004330:Drosophila / Q000235:genetics; D020869:Gene Expression Profiling / Q000706:statistics & numerical data; D006801:Humans; D051379:Mice; D025941:Protein Interaction Mapping / Q000706:statistics & numerical data; D012441:Saccharomyces cerevisiae / Q000235:genetics; D012984:Software; D014157:Transcription Factors / Q000235:genetics; D014158:Transcription, Genetic / Q000502:physiology
chemical_list: D014157:Transcription Factors