Pathway projector

Web-based zoomable pathway browser using KEGG Atlas and Google Maps API

Nobuaki Kono, Kazuharu Arakawa, Ryu Ogawa, Nobuhiro Kido, Kazuki Oshita, Keita Ikegami, Satoshi Tamaki, Masaru Tomita

Research output: Contribution to journalArticle

62 Citations (Scopus)

Abstract

Background: Biochemical pathways provide an essential context for understanding comprehensive experimental data and the systematic workings of a cell. Therefore, the availability of online pathway browsers will facilitate post-genomic research, just as genome browsers have contributed to genomics. Many pathway maps have been provided online as part of public pathway databases. Most of these maps, however, function as the gateway interface to a specific database, and the comprehensiveness of their represented entities, data mapping capabilities, and user interfaces are not always sufficient for generic usage. Methodology/Principal Findings: We have identified five central requirements for a pathway browser: (1) availability of large integrated maps showing genes, enzymes, and metabolites; (2) comprehensive search features and data access; (3) data mapping for transcriptomic, proteomic, and metabolomic experiments, as well as the ability to edit and annotate pathway maps; (4) easy exchange of pathway data; and (5) intuitive user experience without the requirement for installation and regular maintenance. According to these requirements, we have evaluated existing pathway databases and tools and implemented a web-based pathway browser named Pathway Projector as a solution. Conclusions/Significance: Pathway Projector provides integrated pathway maps that are based upon the KEGG Atlas, with the addition of nodes for genes and enzymes, and is implemented as a scalable, zoomable map utilizing the Google Maps API. Users can search pathway-related data using keywords, molecular weights, nucleotide sequences, and amino acid sequences, or as possible routes between compounds. In addition, experimental data from transcriptomic, proteomic, and metabolomic analyses can be readily mapped. Pathway Projector is freely available for academic users at http://www.g-language.org/PathwayProjector/.

Original languageEnglish
Article numbere7710
JournalPLoS One
Volume4
Issue number11
DOIs
Publication statusPublished - 2009 Nov 11

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Atlases
Application programming interfaces (API)
Metabolomics
metabolomics
Databases
transcriptomics
Proteomics
proteomics
genomics
user interface
Aptitude
Enzymes
enzymes
Genomics
Genes
biochemical pathways
Amino Acid Sequence
Language
genes
amino acid sequences

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Pathway projector : Web-based zoomable pathway browser using KEGG Atlas and Google Maps API. / Kono, Nobuaki; Arakawa, Kazuharu; Ogawa, Ryu; Kido, Nobuhiro; Oshita, Kazuki; Ikegami, Keita; Tamaki, Satoshi; Tomita, Masaru.

In: PLoS One, Vol. 4, No. 11, e7710, 11.11.2009.

Research output: Contribution to journalArticle

Kono, Nobuaki ; Arakawa, Kazuharu ; Ogawa, Ryu ; Kido, Nobuhiro ; Oshita, Kazuki ; Ikegami, Keita ; Tamaki, Satoshi ; Tomita, Masaru. / Pathway projector : Web-based zoomable pathway browser using KEGG Atlas and Google Maps API. In: PLoS One. 2009 ; Vol. 4, No. 11.
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