{"id":119,"date":"2022-02-20T17:50:38","date_gmt":"2022-02-20T17:50:38","guid":{"rendered":"http:\/\/localhost\/kpv\/?p=119"},"modified":"2022-02-21T04:23:07","modified_gmt":"2022-02-21T04:23:07","slug":"edges-redundancy","status":"publish","type":"post","link":"https:\/\/dalmolingroup.imd.ufrn.br\/kpv\/edges-redundancy\/","title":{"rendered":"Edges redundancy"},"content":{"rendered":"\n

The KEGG identifies each reaction based on all participant compounds.<\/p>\n\n\n\n

A SER REESCRITO PELO RODRIGO
However, some reactions are very similar, having the same principal substrates and
products. They differ only in secondary compounds.
, differing just in the
secondary compounds. These compounds are highlighted in red in Table 1. This can be a problem
when detecting the APs nodes because the pathway graph will have several pseudo alternatives
routes to bypass a specific point that could be a critical bottleneck<\/mark>.<\/p>\n\n\n\n

For instance, we can take one reaction mediated by the enzyme ec:2.7.1.1, as seen in Figure
below, where four reactions provide the identical product from the same substrate<\/p>\n\n\n\n

\"\"
Example of reaction extracted from the KEGG Glycolysis\/Gluconeogenesis pathway<\/a><\/sup><\/sub><\/figcaption><\/figure>\n\n\n\n

The KEGG canonical pathway is a compilation of many organisms, and some enzymes shown are exclusive for a taxon. In the example above, the enzyme 2.7.1.63 is not present in humans, being used by mycobacterial metabolism [1]. In other cases, the expression of a specific enzyme is tissue-dependent, being predominant in some organs. As an example, hexokinase (2.7.1.1 ) is active in mammalian glucose-dependent tissues, like the heart and brain, and glucokinase (2.7.1.2 ) is found predominantly in the liver [2, 3, 4]. The same occurs with the enzymes 5.1.3.9 and 5.3.1.15, where this last one is founded just in the yeast metabolism [5].
Thus, we need to convert the KEGG\u2019s maps into a graph using a method capable of collapsing the redundant routes inside the pathways, reducing the inaccuracy in the APs detection.<\/p>\n\n\n\n

\"\"
Example of redundant reactions in the Glycolysis\/Gluconeogenesis pathway and respective alias. The compounds considered secondary are highlighted in red.<\/sup><\/sub><\/figcaption><\/figure>\n\n\n\n

[1] M. SZYMONA and W. OSTROWSKI, \u201cINORGANIC POLYPHOSPHATE GLUCOKINASE OF MYCOBACTERIUM PHLEI,\u201d Biochim Biophys Acta, vol. 85, pp. 283\u2013295, May 1964.
[2] J. E. Wilson, Hexokinases, pp. 65\u2013198. Berlin, Heidelberg: Springer Berlin Heidelberg, 1995.
[3] C. Postic, M. Shiota, and M. A. Magnuson, \u201cCell-specific roles of glucokinase in glucose homeostasis,\u201d Recent Prog Horm Res, vol. 56, pp. 195\u2013217, 2001.
[4] J. E. Wilson, \u201cIsozymes of mammalian hexokinase: structure, subcellular localization and metabolic function,\u201d J Exp Biol, vol. 206, pp. 2049\u20132057, Jun 2003.
[5] B. Wurster and B. Hess, \u201cGlucose-6-phosphate-1-epimerase from baker\u2019s yeast. A new enzyme,\u201d FEBS Lett, vol. 23, pp. 341\u2013344, Jul 1972.<\/p>\n","protected":false},"excerpt":{"rendered":"

The KEGG identifies each reaction based on all participant compounds. A SER REESCRITO PELO RODRIGOHowever, some reactions are very similar, having the same principal substrates…<\/p>\n

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