Journal
BIOINFORMATICS
Volume 25, Issue 11, Pages 1470-1471Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btp167
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Funding
- National Genome Research Network [01GS0864]
- German Federal Ministry of Education and Research
- International PhD program of the DKFZ
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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.
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