Skip to main content

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 k 1 dFdC 7.10898534 ± 0.08340605 E
R2 dFdC k 2 dFdCout 0.77373197 ± 0.20074963 E
R3 dFdCout k 3 dFdCMP 0.70443170 ± 0.21974489 P
R4 dFdCMP k 4 dFdCout 2.97694326 ± 1.04080703 P
R5 dFdC k 5 dFdCMP 0.42700844 ± 0.15141087 E
R6 dFdCMP k 6 dFdC 1.05564461 ± 0.29004594 E
R7 dFdCDP k 7 dFdCTP 0.67814401 ± 0.33891991 E
R8 dFdCTP k 8 dFdCDP 0.24600288 ± 0.12911296 E
R9 dFdC k 9 dFdUout 0.07429936 ± 0.10274560 P
R10 dFdUout k 10 dFdC 1.84455256 ± 0.41277353 U
R11 dFdC k 11 dFdU 0.05303525 ± 0.11826494 E
R12 dFdU k 12 dFdC 0.42656017 ± 0.36820500 U
R13 dFdCMP k 13 dFdU 0.01746121 ± 0.04239150 U
R14 dFdU k 14 dFdCMP 1.15296892 ± 0.87614147 U
R15 dFdCDP k 15 dFdU 0.74470692 ± 0.04372718 U
R16 dFdU k 16 dFdCDP 0.13066227 ± 0.30402961 U
R17 dFdCTP k 17 dFdU 0.21526282 ± 0.24385105 U
R18 dFdU k 18 dFdCTP 0.22459952 ± 0.31608938 U
R19 dFdUout k 19 dFdU 0.15238122 ± 0.22702423 E
R20 dFdU k 20 dFdUout 0.90365762 ± 1.15063193 E
R21 dFdCDP k 21 dFdUMP 0.33079357 ± 0.29670272 U
R22 dFdUMP k 22 dFdCDP 0.14176496 ± 0.32573757 U
R23 dFdCTP k 23 dFdUMP 0.03484985 ± 0.08815358 U
R24 dFdUMP k 24 dFdCTP 0.23689470 ± 0.32365144 U
R25 dFdU k 25 dFdUMP 1.30633488 ± 0.31031032 E
R26 dFdUMP k 26 dFdU 1.10583395 ± 0.20384256 E
R27 dFdUout k 27 dFdUDP 0.19345312 ± 1.03917708 P
R28 dFdUDP k 28 dFdUout 0.74875449 ± 1.17435092 P
R29 dFdC k 29 dFdUTP 0.12752520 ± 0.13267091 U
R30 dFdUTP k 30 dFdC 0.99825505 ± 0.40035050 U
R31 dFdCMP k 31 dFdUTP 0.52124642 ± 0.95261538 U
R32 dFdUTP k 32 dFdCMP 0.46822249 ± 0.95099997 U
  1. 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 dFdCMPdFdU(i.e. reaction E13 in Table 6) has been not detected.