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The following maps were obtained by Cytoscape extraction with the ontology databases
Maps
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Ontology || Type || Updated on || Pathways/Genes
REACTOME || Pathways || 17.02.2018 || 2155/10609 (Croft et al., 2010) KEGG || COMPOUND || 16.02.2018 || 267/3657 (Hattori et al., 2003) KEGG || KEGG || 16.02.2018 || 316/7325 (Hattori et al., 2003) GO || Molecular Function || 16.02.2018 || 4612/17556 (Hill et al., 2008) GO || Cellular Component || 16.02.2018 || 1924/18620 (Hill et al., 2008) GO || Immune System || 16.02.2018 || 1170/3152 (Diehl et al., 2007) GO || Biological Process || 16.02.2018 || 15785/17540 (Botstein et al., 2000) References Bindea, G., Mlecnik, B., Hackl, H., Charoentong, P., Tosolini, M., Kirilovsky, A., ... & Galon, J. (2009). ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics, 25(8), 1091-1093. Botstein, D., Cherry, J. M., Ashburner, M., Ball, C. A., Blake, J. A., Butler, H., ... & Eppig, J. T. (2000). Gene Ontology: tool for the unification of biology. Nat genet, 25(1), 25-9. Croft, D., O’kelly, G., Wu, G., Haw, R., Gillespie, M., Matthews, L., ... & Jupe, S. (2010). Reactome: a database of reactions, pathways and biological processes. Nucleic acids research, 39(suppl_1), D691-D697. Diehl, A. D., Lee, J. A., Scheuermann, R. H., & Blake, J. A. (2007). Ontology development for biological systems: immunology. Bioinformatics, 23(7), 913-915. Hattori, M., Okuno, Y., Goto, S., & Kanehisa, M. (2003). Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways. Journal of the American Chemical Society, 125(39), 11853-11865. Hill, D. P., Smith, B., McAndrews-Hill, M. S., & Blake, J. A. (2008, April). Gene Ontology annotations: what they mean and where they come from. In BMC bioinformatics (Vol. 9, No. 5, p. S2). BioMed Central. |