KEGGscape: a Cytoscape app for pathway data integration

F1000Research - Tập 3 - Trang 144
Kozo Nishida1,2, Keiichiro Ono3, Shigehiko Kanaya4, Koichi Takahashi2
1JST, National Bioscience Database Center (NBDC), Tokyo, 102-0081
2Laboratory for Biochemical Simulation, RIKEN Quantitative Biology Center, Osaka, 565-0874
3Department of Medicine, University of California, San Diego, La Jolla, CA 92093
4Graduate School of Information Science, Nara Institute of Science and Technology, Nara, 630-0101

Tóm tắt

In this paper, we present KEGGscape a pathway data integration and visualization app for Cytoscape (http://apps.cytoscape.org/apps/keggscape). KEGG is a comprehensive public biological database that contains large collection of human curated pathways. KEGGscape utilizes the database to reproduce the corresponding hand-drawn pathway diagrams with as much detail as possible in Cytoscape. Further, it allows users to import pathway data sets to visualize biologist-friendly diagrams using the Cytoscape core visualization function (Visual Style) and the ability to perform pathway analysis with a variety of Cytoscape apps. From the analyzed data, users can create complex and interactive visualizations which cannot be done in the KEGG PATHWAY web application. Experimental data with Affymetrix E. coli chips are used as an example to demonstrate how users can integrate pathways, annotations, and experimental data sets to create complex visualizations that clarify biological systems using KEGGscape and other Cytoscape apps.

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Tài liệu tham khảo

M Kanehisa, 2014, Data, information, knowledge and principle: back to metabolism in KEGG., Nucleic Acids Res., 42, D199-D205, 10.1093/nar/gkt1076

N Kono, 2009, Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API., PLoS One., 4, e7710, 10.1371/journal.pone.0007710

T Yamada, 2011, ipath2.0: interactive pathway explorer., Nucleic Acids Res., 39, W412-W415, 10.1093/nar/gkr313

M DeJongh, 2012, CytoSEED: a Cytoscape plugin for viewing, manipulating and analyzing metabolic models created by the model SEED., Bioinformatics., 28, 891-892, 10.1093/bioinformatics/btr719

C Wrzodek, 2011, KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats., Bioinformatics., 27, 2314-2315, 10.1093/bioinformatics/btr377

P Shannon, 2003, Cytoscape: a software environment for integrated models of biomolecular interaction networks., Genome Res., 13, 2498-2504, 10.1101/gr.1239303

M Smoot, 2011, Cytoscape 2.8: new features for data integration and network visualization., Bioinformatics., 27, 431-432, 10.1093/bioinformatics/btq675

S Maere, 2005, BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks., Bioinformatics., 21, 3448-3449, 10.1093/bioinformatics/bti551

G Scardoni, 2009, Analyzing biological network parameters with CentiScaPe., Bioinformatics., 25, 2857-2859, 10.1093/bioinformatics/btp517

H Rohn, 2012, VANTED v2: a framework for systems biology applications., BMC Syst Biol., 6, 139, 10.1186/1752-0509-6-139

Z Hu, 2013, VisANT 4.0: Integrative network platform to connect genes, drugs, diseases and therapies., Nucleic Acids Res., 41, W225-W231, 10.1093/nar/gkt401

R Gentleman, 2004, Bioconductor: open software development for computational biology and bioinformatics., Genome Biol., 5, R80, 10.1186/gb-2004-5-10-r80

L Gautier, ecoliLeucine

L Gautier, 2004, affy--analysis of Affymetrix GeneChip data at the probe level., Bioinformatics., 20, 307-315, 10.1093/bioinformatics/btg405

S Hung, 2002, Global gene expression profiling in Escherichia coli K12. The effects of Leucine-responsive regulatory protein., J Biol Chem., 277, 40309-40323, 10.1074/jbc.M204044200

R Gentleman, genefilter: methods for filtering genes from high-throughput experiments

K Nishida, 2014, F1000Research/KEGGscape., ZENODO., 10.5281/zenodo.10560

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