Inferring biochemical reaction pathways: the case of the gemcitabine pharmacokinetics

Lecca, Paola; Morpurgo, Daniele; Fantaccini, Gianluca; Casagrande, Alessandro; Priami, Corrado

doi:10.1186/1752-0509-6-51

BMC Systems Biology

Table 4 Set of reactions inferred by the time-lagged correlation inference method from synthetic time series data: we denote with the letter “E” the expected reactions, and with a letter “U” those unexpected and incorrect, and with the letter P those reactions that are unexpected but that can be easily explained and are plausible in terms of correlation; the reaction dFdCMP →dFdU (i.e. reaction E13 in Table 6) has been not detected

From: Inferring biochemical reaction pathways: the case of the gemcitabine pharmacokinetics

Reaction ID	Reaction	Rate constant (k ± Δk)	Expected/Unexpected
R1	dFdCout $\overset{k_{1}}{\to}$ dFdC	7.10898534 ± 0.08340605	E
R2	dFdC $\overset{k_{2}}{\to}$ dFdCout	0.77373197 ± 0.20074963	E
R3	dFdCout $\overset{k_{3}}{\to}$ dFdCMP	0.70443170 ± 0.21974489	P
R4	dFdCMP $\overset{k_{4}}{\to}$ dFdCout	2.97694326 ± 1.04080703	P
R5	dFdC $\overset{k_{5}}{\to}$ dFdCMP	0.42700844 ± 0.15141087	E
R6	dFdCMP $\overset{k_{6}}{\to}$ dFdC	1.05564461 ± 0.29004594	E
R7	dFdCDP $\overset{k_{7}}{\to}$ dFdCTP	0.67814401 ± 0.33891991	E
R8	dFdCTP $\overset{k_{8}}{\to}$ dFdCDP	0.24600288 ± 0.12911296	E
R9	dFdC $\overset{k_{9}}{\to}$ dFdUout	0.07429936 ± 0.10274560	P
R10	dFdUout $\overset{k_{10}}{\to}$ dFdC	1.84455256 ± 0.41277353	U
R11	dFdC $\overset{k_{11}}{\to}$ dFdU	0.05303525 ± 0.11826494	E
R12	dFdU $\overset{k_{12}}{\to}$ dFdC	0.42656017 ± 0.36820500	U
R13	dFdCMP $\overset{k_{13}}{\to}$ dFdU	0.01746121 ± 0.04239150	U
R14	dFdU $\overset{k_{14}}{\to}$ dFdCMP	1.15296892 ± 0.87614147	U
R15	dFdCDP $\overset{k_{15}}{\to}$ dFdU	0.74470692 ± 0.04372718	U
R16	dFdU $\overset{k_{16}}{\to}$ dFdCDP	0.13066227 ± 0.30402961	U
R17	dFdCTP $\overset{k_{17}}{\to}$ dFdU	0.21526282 ± 0.24385105	U
R18	dFdU $\overset{k_{18}}{\to}$ dFdCTP	0.22459952 ± 0.31608938	U
R19	dFdUout $\overset{k_{19}}{\to}$ dFdU	0.15238122 ± 0.22702423	E
R20	dFdU $\overset{k_{20}}{\to}$ dFdUout	0.90365762 ± 1.15063193	E
R21	dFdCDP $\overset{k_{21}}{\to}$ dFdUMP	0.33079357 ± 0.29670272	U
R22	dFdUMP $\overset{k_{22}}{\to}$ dFdCDP	0.14176496 ± 0.32573757	U
R23	dFdCTP $\overset{k_{23}}{\to}$ dFdUMP	0.03484985 ± 0.08815358	U
R24	dFdUMP $\overset{k_{24}}{\to}$ dFdCTP	0.23689470 ± 0.32365144	U
R25	dFdU $\overset{k_{25}}{\to}$ dFdUMP	1.30633488 ± 0.31031032	E
R26	dFdUMP $\overset{k_{26}}{\to}$ dFdU	1.10583395 ± 0.20384256	E
R27	dFdUout $\overset{k_{27}}{\to}$ dFdUDP	0.19345312 ± 1.03917708	P
R28	dFdUDP $\overset{k_{28}}{\to}$ dFdUout	0.74875449 ± 1.17435092	P
R29	dFdC $\overset{k_{29}}{\to}$ dFdUTP	0.12752520 ± 0.13267091	U
R30	dFdUTP $\overset{k_{30}}{\to}$ dFdC	0.99825505 ± 0.40035050	U
R31	dFdCMP $\overset{k_{31}}{\to}$ dFdUTP	0.52124642 ± 0.95261538	U
R32	dFdUTP $\overset{k_{32}}{\to}$ dFdCMP	0.46822249 ± 0.95099997	U

The rate constants have been estimated with KInfer. Theirs values are reported with a precision of 8 digits. The third column of the table denote with the letter “E” the expected reactions, and with a letter “U” those unexpected and incorrect, and with the letter “P” those reactions that are unexpected but that can be easily explained and are plausible in terms of correlation. The reaction dFdCMP→dFdU(i.e. reaction E13 in Table 6) has been not detected.

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ISSN: 1752-0509

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