KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor. Export

@article{citeulike:4213034, abstract = {MOTIVATION: KEGG PATHWAY is a service of Kyoto Encyclopedia of Genes and Genomes (KEGG), constructing manually curated pathway maps that represent current knowledge on biological networks in graph models. While valuable graph tools have been implemented in R/Bioconductor, to our knowledge there is currently no software package to parse and analyze KEGG pathways with graph theory. RESULTS: We introduce the software package KEGGgraph in R and Bioconductor, an interface between KEGG pathways and graph models as well as a collection of tools for these graphs. Superior to existing approaches, KEGGgraph captures the pathway topology and allows further analysis or dissection of pathway graphs. We demonstrate the use of the package by the case study of analyzing human pancreatic cancer pathway. AVAILABILITY: KEGGgraph is freely available at the Bioconductor web site (http://www.bioconductor.org). KGML files can be downloaded from KEGG FTP site (ftp://ftp.genome.jp/pub/kegg/xml).}, author = {Zhang, Jitao David D. and Wiemann, Stefan}, citeulike-article-id = {4213034}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btp167}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/11/1470?rss=1}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/19307239}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=19307239}, day = {1}, doi = {10.1093/bioinformatics/btp167}, issn = {1367-4811}, journal = {Bioinformatics (Oxford, England)}, keywords = {bioconductor, graph\_approach, pathway, software}, month = {June}, number = {11}, pages = {1470--1471}, posted-at = {2009-11-15 16:22:00}, priority = {2}, title = {KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor.}, url = {http://dx.doi.org/10.1093/bioinformatics/btp167}, volume = {25}, year = {2009} }

TY - JOUR ID - citeulike:4213034 L3 - citeulike-article-id:4213034 N2 - MOTIVATION: KEGG PATHWAY is a service of Kyoto Encyclopedia of Genes and Genomes (KEGG), constructing manually curated pathway maps that represent current knowledge on biological networks in graph models. While valuable graph tools have been implemented in R/Bioconductor, to our knowledge there is currently no software package to parse and analyze KEGG pathways with graph theory. RESULTS: We introduce the software package KEGGgraph in R and Bioconductor, an interface between KEGG pathways and graph models as well as a collection of tools for these graphs. Superior to existing approaches, KEGGgraph captures the pathway topology and allows further analysis or dissection of pathway graphs. We demonstrate the use of the package by the case study of analyzing human pancreatic cancer pathway. AVAILABILITY: KEGGgraph is freely available at the Bioconductor web site (http://www.bioconductor.org). KGML files can be downloaded from KEGG FTP site (ftp://ftp.genome.jp/pub/kegg/xml). IS - 11 JF - Bioinformatics (Oxford, England) SN - 1367-4811 EP - 1471 TI - KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor. VL - 25 SP - 1470 KW - bioconductor KW - graph_approach KW - pathway KW - software AU - Zhang, Jitao David AU - Wiemann, Stefan PY - 2009/06/01/ UR - http://dx.doi.org/10.1093/bioinformatics/btp167 ER -