The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor
Open accessAbstract
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). Contact: j.zhang@dkfz-heidelberg.de Supplementary information: Supplementary data are available at Bioinformatics online.
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Cites
Cytoscape: A software Environment for integrated models of biomolecular interaction networks
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003) · Genome Research · doi:10.1101/gr.1239303 · Cited by 51,888
Cited by
Pathview: an R/Bioconductor package for pathway-based data integration and visualization
Luo, W., & Brouwer, C. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt285 · Cited by 2,284
Molecular phenomics and metagenomics of hepatic steatosis in non-diabetic obese women
Hoyles, L., Fernández-Real, J.-M., Federici, M., Serino, M., Abbott, J., Charpentier, J., Heymes, C., Luque, J. L., Anthony, E., Barton, R. H., et al. (2018) · Nature Medicine · doi:10.1038/s41591-018-0061-3 · Cited by 720
Hoyles, L., Pontifex, M. G., Rodriguez-Ramiro, I., Anis-Alavi, M. A., Jelane, K. S., Snelling, T., Solito, E., Fonseca, S., Carvalho, A. L., Carding, S. R., et al. (2021) · Microbiome · doi:10.1186/s40168-021-01181-z · Cited by 221
csuWGCNA: a combination of signed and unsigned WGCNA to capture negative correlations
Dai, R., Xia, Y., Liu, C., & Chen, C. (2018) · doi:10.1101/288225 · Cited by 13
(2021) · doi:10.1101/2021.01.28.428430 · Cited by 7
Metadata
- Authors
- Zhang, J. D., & Wiemann, S.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-03-23
- Volume
- 25
- Issue
- 11
- Pages
- 1470-1471
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2100625056
- Cited by
- 331
- References
- 1
- FWCI
- 5.04
- Type
- journal article
- Language
- en
- Open access
- hybrid
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