BioModelsapplication/xmlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000093?filename=BIOMD0000000093.pdfhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000093?filename=BIOMD0000000093-biopax3.owlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000093?filename=BIOMD0000000093-biopax2.owlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000093?filename=BIOMD0000000093_url.xmlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000093?filename=BIOMD0000000093_urn.xmlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000093?filename=BIOMD0000000093.scihttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000093?filename=BIOMD0000000093.pnghttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000093?filename=BIOMD0000000093.xpphttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000093?filename=BIOMD0000000093.vcmlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000093?filename=BIOMD0000000093.mprimaryOK200Sharat VayttadenManually curatedL2V1https://www.ebi.ac.uk/biomodels/BIOMD000000009312527385falseBioModelsSBMLModelsYamada2003 JAK STAT pathway2003MODEL4879478021Yamada S, Shiono S, Joo A, Yoshimura AYamada S12527385,
Suppressor of cytokine signaling-1 (SOCS1) was identified as the negative regulator of Janus kinase (JAK) and signal transducer and activator of transcription (STAT) signal transduction pathway. However, the kinetics and control mechanism of the pathway have not yet been fully understood. We have developed the computer simulation of the JAK/STAT pathway. Without nuclear phosphatase, SOCS1's binding to JAK did not cause the decrease in nuclear phosphorylated STAT1. However, without SH2 domain-containing tyrosine phosphatase 2 (SHP-2) or cytoplasmic phosphatase, it did. So nuclear phosphatase is considered to be the most important in this system. By changing parameters of the model, dynamical characteristics and control mechanism were investigated.. null, 534.
Advanced Technology R&D Center, Mitsubishi Electric Corporation, 8-1-1, Tsukaguchi-Honmachi, Amagasaki, Hyogo 661-8661, Japan. yamada.satoshi@wrc.melco.co.jpdoqcs@ncbs.res.inDOQCSBIOMD0000000093Suppressor of cytokine signaling-1 (SOCS1) was identified as the negative regulator of Janus kinase (JAK) and signal transducer and activator of transcription (STAT) signal transduction pathway. However, the kinetics and control mechanism of the pathway have not yet been fully understood. We have developed the computer simulation of the JAK/STAT pathway. Without nuclear phosphatase, SOCS1's binding to JAK did not cause the decrease in nuclear phosphorylated STAT1. However, without SH2 domain-containing tyrosine phosphatase 2 (SHP-2) or cytoplasmic phosphatase, it did. So nuclear phosphatase is considered to be the most important in this system. By changing parameters of the model, dynamical characteristics and control mechanism were investigated.Control mechanism of JAK/STAT signal transduction pathway.Yamada Satoshi S, Shiono Satoru S, Joo Akiko A, Yoshimura Akihiko ASignal Transduction Systems, transcription, Signal Transductions, para Tyrosine, 19-106, Hop1, anon-WO03040301.207, DmelCG3954, STAT91, EG:BACN25G24.2, Receptor-Mediated, jak, Signal Transduction System, In silico Modeling, anon-WO03040301.209, jan, XStat1, Computer, l(1)csw, body system, Receptor Mediated Signal Transduction, Signal Transduction, HOP, Hop, l(1)L4, SHP-2, system, 4, Computerized Models, anon-WO03040301.219, Kinase, Csw/Shp2, Protein-tyrosine phosphatase SYP, protein-tyrosine kinase activity, Cell Signaling, Models, l(1)GA114, CIS1, Phosphotransferase, TIP3, signal transduction by protein phosphorylation, DmelCG1594, Shp-2, Tum-1, anatomical systems, CANDF7, reference sample, In silico Models, SSI1, ligand, 2-amino-3-(4-hydroxyphenyl)propanoic acid, 3-(p-Hydroxyphenyl)alanine, Transducer, Signal, Pathways, l(1)2Db, l(1)2Dd, Signal Pathways, SAP-2, Transphosphorylase, Y, Signal Transduction Pathway, l(1)hop, Computational, DNA-dependent, signalling pathway, L4, L Tyrosine, SOCS-1, Tyr, Computer Model, Janus kinase activity, AA408197, Protein G18, CG7933, PTP1D, signal transduction by cis-phosphorylation, Signal Transduction Pathways, Transductions, Tyrosin, Controlled., ATP Phosphotransferases, Model, transcription from bacterial-type RNA polymerase promoter, In silico, In silico Model, Signal Pathway, phosphatase, jan A, sh2, SH2, ATP, Controlled, SH-PTP3, SH-PTP2, CISH1, cellular transcription, Controlling, Pathway, AW536184, DNA-dependent transcription, sh-2, Shp2/csw, 2-Amino-3-(p-hydroxyphenyl)propionic acid, signal transduction by conformational transition, In silico Simulation, Receptor-Mediated Signal Transductions, PTP2C, para-Tyrosine, Computational Modelling, l(1)G0170, Protein-tyrosine phosphatase 1D, Computer Simulations, PTP-1D, Phosphotransferases, signal transduction by trans-phosphorylation, Computerized, Tyrosine, Simulations, DD6G4-4, signaling cascade, tirosina, ISGF-3, Syp, CIS, Receptor-Mediated Signal Transduction, Computer Models, Systems, BcDNA:AT12574, 3.1.3.48, connected anatomical system, signalling cascade, regulator, Protein-tyrosine phosphatase 2C, Transduction, PTP-2C, tyrosine, d-jak, CG3954, DmelCG7933, CIS-1, Transphosphorylases, DmHD-160, Kinases, 2010005J02Rik, Modeling, System, 2700084A17Rik, Shp2, L-isomer, DNA-templated, Computerized Model, phosphoric monoester hydrolase activity, E(sev)1A, Cish1, Computational Modeling, Modelling, Cish7, L isomer, organ system, Dm JAK, CSW, Csw, signaling pathway, SOCS, JAB, HD-160, IMD31B, IMD31C, bacterial transcription, Tum, IMD31A, msvl, l(1)G18, Simulation, L-Tyrosine, SSI-1, JAK, Jak, Jan, janus, CG1594, l(1)10Be, Suppressor of cytokine signaling, Myo15aSignal Transduction Systems, Signal Transductions, IPP2A2, Hop1, Receptor-Mediated, jak, Signal Transduction System, 2210402P09Rik, PHAPII, 5730420M11Rik, inadequate, Receptor Mediated Signal Transduction, IFNA13, Signal Transduction, HOP, Hop, l(1)L4, template-activating factor I, 4, protein-tyrosine kinase activity, Cell Signaling, CIS1, TIP3, PIST, signal transduction by protein phosphorylation, DmelCG1594, DmelCG7615, SET, Tum-1, reference sample, IFN-alphaD, TAF-I, SSI1, phosphatase 2A inhibitor I2PP2A, ipp2a2, Signal, AI844555, Pathways, 2pp2a, present in organism, Signal Pathways, Signal Transduction Pathway, l(1)hop, CG10574, DEPP, DmelCG4299, set, IGAAD, signalling pathway, 2PP2A, L4, DmelCG10574, taf-ibeta, SOCS-1, Janus kinase activity, Fseg, dSET, dSet, Protein G18, signal transduction by cis-phosphorylation, Signal Transduction Pathways, Transductions, Signal Pathway, Controlled, Decidual protein induced by progesterone, phapii, Controlling, CISH1, Pathway, Papers, igaad, signal transduction by conformational transition, Receptor-Mediated Signal Transductions, StF-IT-1, IFNA@, results, signal transduction by trans-phosphorylation, Copyrights., signaling cascade, Fasting-induced gene protein, I-2PP2A, CIS, Receptor-Mediated Signal Transduction, Systems, Dm I-2, CAL, I2PP2A, signalling cascade, regulator, Transduction, GOPC1, d-jak, Data Base, CIS-1, DmHD-160, figures, HLA-DR-associated protein II, DI-2, System, IFL, I-2Dm, IFN, Cish1, CG4299, inhibitor of granzyme A-activated DNase, Cish7, dJ94G16.2, I-2PP1, dSET/TAF-Ibeta, Dm JAK, FIG, 2610030F17Rik, Comments, TAF-IBETA, signaling pathway, HD-160, JAB, SOCS, concentration, Tum, msvl, CG7615, l(1)G18, TAF-Ibeta, JAK, Jak, SSI-1, CG1594, l(1)10Be, Suppressor of cytokine signaling, AA407739, i2pp2a, IFN-ALPHASignal Transduction Systems, Controlling, Signal Transductions, Pathway, Hop1, Receptor-Mediated, signal transduction by conformational transition, Receptor-Mediated Signal Transductions, jak, Signal Transduction System, signal transduction by trans-phosphorylation, Receptor Mediated Signal Transduction, Signal Transduction, signaling cascade, HOP, Hop, l(1)L4, Receptor-Mediated Signal Transduction, Systems, 4, protein-tyrosine kinase activity, signalling cascade, Cell Signaling, Transduction, d-jak, signal transduction by protein phosphorylation, DmelCG1594, DmHD-160, Tum-1, reference sample, System, Signal, Pathways, Signal Pathways, Signal Transduction Pathway, l(1)hop, Dm JAK, signalling pathway, L4, signaling pathway, HD-160, Signal Pathway., Tum, Janus kinase activity, msvl, signal transduction by cis-phosphorylation, l(1)G18, Signal Transduction Pathways, JAK, Jak, Transductions, CG1594, l(1)10Be, ControlledfalseYamada2003_JAK_STAT_pathway
NCBS Curation Comments
This model shows the control mechanism of Jak-Stat pathway, here SOCS1 (Suppressor of cytokine signaling-I) was identified as the negative regulator of Jak and STAT signal transduction pathway. Note: There are a few ambiguities in the paper like initial concentration of IFN and some reactions were missing in the paper that were employed for obtaining the results. The graphs are almost similar to the graphs as shown in the paper but still some ambiguities regarding the concentration are there. Thanks to Dr Satoshi Yamada for clarifying some of those ambiguities and providing the values used in simulations.
Biomodels Curation Comments
The model reproduces Fig 2 (A,C,E,G,I,K,M) of the paper. The set of equations present in the paper are inadequate to reproduce the figures mentioned . The model appears to have been fine tuned after correspondence between the curators at NCBS and the authors. There is however a slight discrepancy between the simulation results and the plots in the paper. The model was tested on MathSBML.
This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2006 The BioModels Team.
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2012-05-162007-03-072007-03-13BIOMD0000000093R02584R025852.7.10.23.1.3.48mmu0463012527385CHEBI:33699MODEL4879478021BIOMD0000000093GO:0007259GO:0005737GO:0005634GO:0005515GO:0005133GO:0019964GO:0004906GO:0007171GO:0004713GO:0007260GO:0007261GO:0019902GO:0005001GO:0042512GO:0007262GO:0065002GO:0006351GO:0006406GO:0006412GO:0006402GO:0044257GO:0043624C0004610090O88507P52332P01572P42225P35235O35716IPR009127IPR001217IPR000980IPR001496