Nucleic Acids Research Advance Access originally published online on June 22, 2007
Nucleic Acids Research 2007 35(Web Server issue):W625-W632; doi:10.1093/nar/gkm295
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Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W625-W632
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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VisANT 3.0: new modules for pathway visualization, editing, prediction and construction
1Center for Advanced Genomic Technology, Boston University, Boston, MA 02215, USA, 2Bioinformatics Center, Institute for Chemical Research, Kyoto University, Japan, 3Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA and 4Human Genome Center, Institute of Medical Science, University of Tokyo, Japan
*To whom correspondence should be addressed. Tel: +617 353 1122; Fax: +617 353 3333; Email: delisi{at}bu.edu
Received January 31, 2007. Revised April 9, 2007. Accepted April 12, 2007.
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.
Present address: Joe Mellor, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
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