Cited by 77Bioinformatics and Genomic NetworksGenomics and Phylogenetic StudiesBiomedical Text Mining and Ontologies

VisANT 3.0: new modules for pathway visualization, editing, prediction and construction

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Hu, Zhenjun, Ng, David M., Yamada, Takuji, Chen, Chunnuan, Kawashima, Shuichi, Mellor, Joe, Linghu, Bolan, Kanehisa, Minoru +2 more·2007·Nucleic Acids Research

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.

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  • Over 300 pathway or molecular interaction related data resources and many visualization and analysis software tools have been developed.

    “Over 300 pathway or molecular interaction related data resources17 and many visualization and analysis software tools3,20-22 have been developed.”

    From The BioPAX community standard for pathway data sharing (2010) · cites this paper as [22]

  • ChiBE and VisANT pathway visualization tools read BioPAX format.

    “For instance, the ChiBE and VisANT pathway visualization tools read BioPAX format22 and the WikiPathways website53, a community wiki for pathways, is working on using BioPAX to help import pathways from numerous sources, including manually edited pathways from biologists.”

    From The BioPAX community standard for pathway data sharing (2010) · cites this paper as [22]

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Authors
Hu, Z., Ng, D. M., Yamada, T., Chen, C., Kawashima, S., Mellor, J., Linghu, B., Kanehisa, M., Stuart, J. M., & DeLisi, C.
Affiliations
Boston University (US)
Corresponding author
DeLisi, Charles
Venue
Nucleic Acids Research
Published
2007-07
Volume
35
Issue
suppl_2
Pages
W625-W632
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
OpenAlex
W2089691764
Cited by
76
References
37
Citations by year
2024: 1 · 2022: 2 · 2020: 1 · 2019: 1 · 2018: 1 · 2017: 3 · 2016: 1 · 2014: 2 · 2013: 6 · 2012: 7
FWCI
5.82
Type
journal article
Language
en
Open access
Locations
  • Nucleic Acids Research (publishedVersion)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • OpenBU (Boston University) (submittedVersion)
Funders
National Center for Research Resources (R01RR022971)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
Keywords
pathway visualization, KEGG, co-expression analysis, gene expression visualization, protein-protein interaction, pathway enrichment, Scalable Vector Graphics
MeSH terms
Animals, Computer Graphics, Database Management Systems, Drosophila, Humans, Saccharomyces cerevisiae, Software, Transcription Factors, Transcription, Genetic, Caenorhabditis elegans, Computational Biology, Gene Expression Profiling, Protein Interaction Mapping, Databases, Genetic, Mice

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