Resources
Resources from KEGG,
Reactome,
WikiPathways, and
MSigDB
have been used to build this package and application.
KEGG
License
KEGG gene sets are downloaded via the KEGG API for
academic purposes (Terms and
conditions). More info at Bio2BEL KEGG.
References
- Kanehisa, Furumichi, M., Tanabe, M., Sato, Y., and Morishima, K.; KEGG: new
perspectives
on genomes, pathways, diseases and drugs. Nucleic Acids Res. 45, D353-D361
(2017).
- Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M., and Tanabe, M.; KEGG as a
reference resource for gene and protein annotation. Nucleic Acids Res. 44,
D457-D462
(2016).
- Kanehisa, M. and Goto, S.; KEGG: Kyoto Encyclopedia of Genes and Genomes.
Nucleic Acids
Res. 28, 27-30 (2000).
Reactome
License
Reactome gene sets are downloaded via the Reactome
API for academic purposes (Terms and
conditions). More info at Bio2BEL
Reactome.
References
- Fabregat, Antonio et al. “The Reactome Pathway Knowledgebase.” Nucleic Acids
Research 44.Database issue (2016): D481–D487. PMC. Web. 6 Oct. 2017.
- Croft, David et al. “The Reactome Pathway Knowledgebase.” Nucleic Acids Research
42.Database issue (2014): D472–D477. PMC. Web. 6 Oct. 2017.
WikiPathways
License
WikiPathways gene sets are downloaded via the WikiPathways
API for academic purposes (Terms and
conditions). More info at Bio2BEL
WikiPathways.
References
- Slenter DN, Kutmon M, Hanspers K, Riutta A, Windsor J, Nunes N, Mélius J, Cirillo E,
Coort SL, Digles D, Ehrhart F, Giesbertz P, Kalafati M, Martens M, Miller R, Nishida
K,
Rieswijk L, Waagmeester A, Eijssen LMT, Evelo CT, Pico AR, Willighagen EL.
WikiPathways:
a multifaceted pathway database bridging metabolomics to other omics research
Nucleic
Acids Research, (2017)doi.org/10.1093/nar/gkx1064
- Kutmon M, Riutta A, Nunes N, Hanspers K, Willighagen EL, Bohler A, Mélius J,
Waagmeester
A, Sinha SR, Miller R, Coort SL, Cirillo E, Smeets B, Evelo CT, Pico AR.
WikiPathways:
capturing the full diversity of pathway knowledge Nucl. Acids Res., 44, D488-D494
(2016)
doi:10.1093/nar/gkv1024
- Kelder T, van Iersel MP, Hanspers K, Kutmon M, Conklin BR, Evelo C, Pico AR.
WikiPathways: building research communities on biological pathways. Nucleic Acids
Res.
2012 Jan;40(Database issue):D1301-7
MSigDB
License
Only MSig gene sets with (CC BY 4.0)
are used in ComPath (Terms and
conditions). More info at Bio2BEL
MSig.
References
- Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette,
M. A., ... & Mesirov, J. P. (2005). Gene set enrichment analysis: a knowledge-based
approach for interpreting genome-wide expression profiles. Proceedings of the
National Academy of Sciences, 102(43), 15545-15550.
Visualization Tools
This application makes use of other dedicated bioinformatics software such as
Clustergrammer and
Cytoscape JS.
References
- Fernandez, N. F. et al. Clustergrammer, a web-based heatmap visualization and
analysis
tool for high-dimensional biological data. Sci. Data 4:170151 doi:
10.1038/sdata.2017.151 (2017).
-
Franz, M., Lopes, C. T., Huck, G., Dong, Y., Sumer, O., & Bader, G. D. (2015).
Cytoscape. js: a graph theory library for visualisation and analysis.
Bioinformatics, 32(2), 309-311.