Pathways Knowlegdes

Biological pathway database

Pathway DOIs Note
Glutathione Metabolism II

Accession ID: PathBank:SMP0001941		 -
Glutathione Metabolism III

Accession ID: PathBank:SMP0002032		 -
Peptidoglycan Biosynthesis II

Accession ID: PathBank:SMP0002074		 -
superpathway of proto- and siroheme biosynthesis

Accession ID: PlantCyc:ARA_PWYQT-62
  • 10.1016/s0378-1119(96)00545-8
  • 10.1046/j.1365-313x.1996.10050883.x
  • 10.1074/jbc.272.5.2744
  • 10.1074/jbc.m411360200
  • 10.1104/pp.107.100065
 Nagai S, Koide M, Takahashi S, Kikuta A, Aono M, Sasaki-Sekimoto Y, Ohta H, Takamiya K, Masuda T. Induction of isoforms of tetrapyrrole biosynthetic enzymes, AtHEMA2 and AtFC1, under stress conditions and their physiological functions in Arabidopsis. Plant Physiol. 2007 Jun;144(2):1039–51. PMID: 17416636; PMCID: PMC1914178.; Raux-Deery E, Leech HK, Nakrieko KA, McLean KJ, Munro AW, Heathcote P, Rigby SE, Smith AG, Warren MJ. Identification and characterization of the terminal enzyme of siroheme biosynthesis from Arabidopsis thaliana: a plastid-located sirohydrochlorin ferrochelatase containing a 2FE-2S center. J Biol Chem. 2005 Feb 11;280(6):4713–21. doi: 10.1074/jbc.m411360200. PMID: 15545265.; Leustek T, Smith M, Murillo M, Singh DP, Smith AG, Woodcock SC, Awan SJ, Warren MJ. Siroheme biosynthesis in higher plants. Analysis of an S-adenosyl-L-methionine-dependent uroporphyrinogen III methyltransferase from Arabidopsis thaliana. J Biol Chem. 1997 Jan 31;272(5):2744–52. doi: 10.1074/jbc.272.5.2744. PMID: 9006913.; Narita S, Tanaka R, Ito T, Okada K, Taketani S, Inokuchi H. Molecular cloning and characterization of a cDNA that encodes protoporphyrinogen oxidase of Arabidopsis thaliana. Gene. 1996 Dec 05;182(1-2):169–75. doi: 10.1016/s0378-1119(96)00545-8. PMID: 8982084.; Sakakibara H, Takei K, Sugiyama T. Isolation and characterization of a cDNA that encodes maize uroporphyrinogen III methyltransferase, an enzyme involved in the synthesis of siroheme, which is prosthetic group of nitrite reductase. Plant J. 1996 Nov;10(5):883–92. doi: 10.1046/j.1365-313x.1996.10050883.x. PMID: 8953249.
tetrapyrrole biosynthesis I (from glutamate)

Accession ID: PlantCyc:ARA_PWY-5188
  • 10.1016/0968-0004(90)90304-t
  • 10.1105/tpc.7.7.1039
 Von Wettstein D, Gough S, Kannangara CG. Chlorophyll Biosynthesis. Plant Cell. 1995 Jul;7(7):1039–57. PMID: 12242396; PMCID: PMC160907.; Warren MJ, Scott AI. Tetrapyrrole assembly and modification into the ligands of biologically functional cofactors. Trends Biochem Sci. 1990 Dec;15(12):486–91. doi: 10.1016/0968-0004(90)90304-t. PMID: 2077690.
superpathay of heme b biosynthesis from glutamate

Accession ID: PlantCyc:ARA_PWY-5918
  • 10.1093/molbev/msi230
 Oborník M, Green BR. Mosaic origin of the heme biosynthesis pathway in photosynthetic eukaryotes. Mol Biol Evol. 2005 Dec;22(12):2343–53. doi: 10.1093/molbev/msi230. PMID: 16093570.
Sensory Perception

Accession ID: Reactome:R-CEL-9709957
  • 10.1002/cphy.c160049
  • 10.1016/b978-0-444-63855-7.00005-8
  • 10.1016/bs.pmbts.2015.06.001
  • 10.1038/nrn.2017.68
  • 10.1242/jcs.175687
  • 10.3389/fncel.2020.595523
 Lankford CK, Laird JG, Inamdar SM, Baker SA. A Comparison of the Primary Sensory Neurons Used in Olfaction and Vision. Front Cell Neurosci. 2020;14():595523. PMID: 33250719; PMCID: PMC7676898.; Glezer I, Malnic B. Olfactory receptor function. Handb Clin Neurol. 2019;164():67–78. doi: 10.1016/b978-0-444-63855-7.00005-8. PMID: 31604564.; Fettiplace R. Hair Cell Transduction, Tuning, and Synaptic Transmission in the Mammalian Cochlea. Comprehensive Physiology. 2017 Oct;7(4):1197–227. doi: 10.1002/j.2040-4603.2017.tb00783.x.; Roper SD, Chaudhari N. Taste buds: cells, signals and synapses. Nature Reviews Neuroscience. 2017 Jun 29;18(8):485–97. doi: 10.1038/nrn.2017.68.; Molday RS, Moritz OL. Photoreceptors at a glance. J Cell Sci. 2015 Nov 15;128(22):4039–45. PMID: 26574505; PMCID: PMC4712787.; Grossniklaus HE, Geisert EE, Nickerson JM. Introduction to the Retina. Prog Mol Biol Transl Sci. 2015;134():383–96. doi: 10.1016/bs.pmbts.2015.06.001. PMID: 26310166.
Sensory Perception

Accession ID: Reactome:R-XTR-9709957
  • 10.1002/cphy.c160049
  • 10.1016/b978-0-444-63855-7.00005-8
  • 10.1016/bs.pmbts.2015.06.001
  • 10.1038/nrn.2017.68
  • 10.1242/jcs.175687
  • 10.3389/fncel.2020.595523
 Lankford CK, Laird JG, Inamdar SM, Baker SA. A Comparison of the Primary Sensory Neurons Used in Olfaction and Vision. Front Cell Neurosci. 2020;14():595523. PMID: 33250719; PMCID: PMC7676898.; Glezer I, Malnic B. Olfactory receptor function. Handb Clin Neurol. 2019;164():67–78. doi: 10.1016/b978-0-444-63855-7.00005-8. PMID: 31604564.; Fettiplace R. Hair Cell Transduction, Tuning, and Synaptic Transmission in the Mammalian Cochlea. Comprehensive Physiology. 2017 Oct;7(4):1197–227. doi: 10.1002/j.2040-4603.2017.tb00783.x.; Roper SD, Chaudhari N. Taste buds: cells, signals and synapses. Nature Reviews Neuroscience. 2017 Jun 29;18(8):485–97. doi: 10.1038/nrn.2017.68.; Molday RS, Moritz OL. Photoreceptors at a glance. J Cell Sci. 2015 Nov 15;128(22):4039–45. PMID: 26574505; PMCID: PMC4712787.; Grossniklaus HE, Geisert EE, Nickerson JM. Introduction to the Retina. Prog Mol Biol Transl Sci. 2015;134():383–96. doi: 10.1016/bs.pmbts.2015.06.001. PMID: 26310166.
Sensory Perception

Accession ID: Reactome:R-SSC-9709957
  • 10.1002/cphy.c160049
  • 10.1016/b978-0-444-63855-7.00005-8
  • 10.1016/bs.pmbts.2015.06.001
  • 10.1038/nrn.2017.68
  • 10.1242/jcs.175687
  • 10.3389/fncel.2020.595523
 Lankford CK, Laird JG, Inamdar SM, Baker SA. A Comparison of the Primary Sensory Neurons Used in Olfaction and Vision. Front Cell Neurosci. 2020;14():595523. PMID: 33250719; PMCID: PMC7676898.; Glezer I, Malnic B. Olfactory receptor function. Handb Clin Neurol. 2019;164():67–78. doi: 10.1016/b978-0-444-63855-7.00005-8. PMID: 31604564.; Fettiplace R. Hair Cell Transduction, Tuning, and Synaptic Transmission in the Mammalian Cochlea. Comprehensive Physiology. 2017 Oct;7(4):1197–227. doi: 10.1002/j.2040-4603.2017.tb00783.x.; Roper SD, Chaudhari N. Taste buds: cells, signals and synapses. Nature Reviews Neuroscience. 2017 Jun 29;18(8):485–97. doi: 10.1038/nrn.2017.68.; Molday RS, Moritz OL. Photoreceptors at a glance. J Cell Sci. 2015 Nov 15;128(22):4039–45. PMID: 26574505; PMCID: PMC4712787.; Grossniklaus HE, Geisert EE, Nickerson JM. Introduction to the Retina. Prog Mol Biol Transl Sci. 2015;134():383–96. doi: 10.1016/bs.pmbts.2015.06.001. PMID: 26310166.
Sensory Perception

Accession ID: Reactome:R-GGA-9709957
  • 10.1002/cphy.c160049
  • 10.1016/b978-0-444-63855-7.00005-8
  • 10.1016/bs.pmbts.2015.06.001
  • 10.1038/nrn.2017.68
  • 10.1242/jcs.175687
  • 10.3389/fncel.2020.595523
 Lankford CK, Laird JG, Inamdar SM, Baker SA. A Comparison of the Primary Sensory Neurons Used in Olfaction and Vision. Front Cell Neurosci. 2020;14():595523. PMID: 33250719; PMCID: PMC7676898.; Glezer I, Malnic B. Olfactory receptor function. Handb Clin Neurol. 2019;164():67–78. doi: 10.1016/b978-0-444-63855-7.00005-8. PMID: 31604564.; Fettiplace R. Hair Cell Transduction, Tuning, and Synaptic Transmission in the Mammalian Cochlea. Comprehensive Physiology. 2017 Oct;7(4):1197–227. doi: 10.1002/j.2040-4603.2017.tb00783.x.; Roper SD, Chaudhari N. Taste buds: cells, signals and synapses. Nature Reviews Neuroscience. 2017 Jun 29;18(8):485–97. doi: 10.1038/nrn.2017.68.; Molday RS, Moritz OL. Photoreceptors at a glance. J Cell Sci. 2015 Nov 15;128(22):4039–45. PMID: 26574505; PMCID: PMC4712787.; Grossniklaus HE, Geisert EE, Nickerson JM. Introduction to the Retina. Prog Mol Biol Transl Sci. 2015;134():383–96. doi: 10.1016/bs.pmbts.2015.06.001. PMID: 26310166.
Sensory Perception

Accession ID: Reactome:R-DME-9709957
  • 10.1002/cphy.c160049
  • 10.1016/b978-0-444-63855-7.00005-8
  • 10.1016/bs.pmbts.2015.06.001
  • 10.1038/nrn.2017.68
  • 10.1242/jcs.175687
  • 10.3389/fncel.2020.595523
 Lankford CK, Laird JG, Inamdar SM, Baker SA. A Comparison of the Primary Sensory Neurons Used in Olfaction and Vision. Front Cell Neurosci. 2020;14():595523. PMID: 33250719; PMCID: PMC7676898.; Glezer I, Malnic B. Olfactory receptor function. Handb Clin Neurol. 2019;164():67–78. doi: 10.1016/b978-0-444-63855-7.00005-8. PMID: 31604564.; Fettiplace R. Hair Cell Transduction, Tuning, and Synaptic Transmission in the Mammalian Cochlea. Comprehensive Physiology. 2017 Oct;7(4):1197–227. doi: 10.1002/j.2040-4603.2017.tb00783.x.; Roper SD, Chaudhari N. Taste buds: cells, signals and synapses. Nature Reviews Neuroscience. 2017 Jun 29;18(8):485–97. doi: 10.1038/nrn.2017.68.; Molday RS, Moritz OL. Photoreceptors at a glance. J Cell Sci. 2015 Nov 15;128(22):4039–45. PMID: 26574505; PMCID: PMC4712787.; Grossniklaus HE, Geisert EE, Nickerson JM. Introduction to the Retina. Prog Mol Biol Transl Sci. 2015;134():383–96. doi: 10.1016/bs.pmbts.2015.06.001. PMID: 26310166.
Cation-coupled Chloride cotransporters

Accession ID: Reactome:R-SPO-426117
  • 10.1007/s00424-003-1066-3
  • 10.1152/physrev.00011.2004
 Gamba G. Molecular physiology and pathophysiology of electroneutral cation-chloride cotransporters. Physiol Rev. 2005 Apr;85(2):423–93. doi: 10.1152/physrev.00011.2004. PMID: 15788703.; Hebert SC, Mount DB, Gamba G. Molecular physiology of cation-coupled Cl- cotransport: the SLC12 family. Pflügers Archiv - European Journal of Physiology. 2003 May 09;447(5):580–93. doi: 10.1007/s00424-003-1066-3.
Sensory perception of salty taste

Accession ID: Reactome:R-XTR-9730628
  • 10.1002/ana.21895
  • 10.1007/s00424-014-1683-z
  • 10.1016/j.neuron.2020.03.006
  • 10.1093/chemse/bjaa004
  • 10.1093/chemse/bjh002
  • 10.3390/nu12041195
 Nomura K, Nakanishi M, Ishidate F, Iwata K, Taruno A. All-Electrical Ca2+-Independent Signal Transduction Mediates Attractive Sodium Taste in Taste Buds. Neuron. 2020 Jun 03;106(5):816–829.e6. doi: 10.1016/j.neuron.2020.03.006. PMID: 32229307.; Bigiani A. Does ENaC Work as Sodium Taste Receptor in Humans? Nutrients. 2020 Apr 24;12(4). PMID: 32344597; PMCID: PMC7230849.; Lossow K, Hermans-Borgmeyer I, Meyerhof W, Behrens M. Segregated Expression of ENaC Subunits in Taste Cells. Chem Senses. 2020 May 21;45(4):235–48. doi: 10.1093/chemse/bjaa004. PMID: 32006019.; Roper SD. The taste of table salt. Pflügers Archiv - European Journal of Physiology. 2015 Jan 07;467(3):457–63. doi: 10.1007/s00424-014-1683-z.; Estacion M, Harty TP, Choi JS, Tyrrell L, Dib-Hajj SD, Waxman SG. A sodium channel gene SCN9A polymorphism that increases nociceptor excitability. Ann Neurol. 2009 Dec;66(6):862–6. doi: 10.1002/ana.21895. PMID: 20033988.; Rossier O, Cao J, Huque T, Spielman AI, Feldman RS, Medrano JF, Brand JG, le Coutre J. Analysis of a human fungiform papillae cDNA library and identification of taste-related genes. Chem Senses. 2004 Jan;29(1):13–23. doi: 10.1093/chemse/bjh002. PMID: 14752036.
Sensory perception of salty taste

Accession ID: Reactome:R-SSC-9730628
  • 10.1002/ana.21895
  • 10.1007/s00424-014-1683-z
  • 10.1016/j.neuron.2020.03.006
  • 10.1093/chemse/bjaa004
  • 10.1093/chemse/bjh002
  • 10.3390/nu12041195
 Nomura K, Nakanishi M, Ishidate F, Iwata K, Taruno A. All-Electrical Ca2+-Independent Signal Transduction Mediates Attractive Sodium Taste in Taste Buds. Neuron. 2020 Jun 03;106(5):816–829.e6. doi: 10.1016/j.neuron.2020.03.006. PMID: 32229307.; Bigiani A. Does ENaC Work as Sodium Taste Receptor in Humans? Nutrients. 2020 Apr 24;12(4). PMID: 32344597; PMCID: PMC7230849.; Lossow K, Hermans-Borgmeyer I, Meyerhof W, Behrens M. Segregated Expression of ENaC Subunits in Taste Cells. Chem Senses. 2020 May 21;45(4):235–48. doi: 10.1093/chemse/bjaa004. PMID: 32006019.; Roper SD. The taste of table salt. Pflügers Archiv - European Journal of Physiology. 2015 Jan 07;467(3):457–63. doi: 10.1007/s00424-014-1683-z.; Estacion M, Harty TP, Choi JS, Tyrrell L, Dib-Hajj SD, Waxman SG. A sodium channel gene SCN9A polymorphism that increases nociceptor excitability. Ann Neurol. 2009 Dec;66(6):862–6. doi: 10.1002/ana.21895. PMID: 20033988.; Rossier O, Cao J, Huque T, Spielman AI, Feldman RS, Medrano JF, Brand JG, le Coutre J. Analysis of a human fungiform papillae cDNA library and identification of taste-related genes. Chem Senses. 2004 Jan;29(1):13–23. doi: 10.1093/chemse/bjh002. PMID: 14752036.
Sensory perception of salty taste

Accession ID: Reactome:R-CFA-9730628
  • 10.1002/ana.21895
  • 10.1007/s00424-014-1683-z
  • 10.1016/j.neuron.2020.03.006
  • 10.1093/chemse/bjaa004
  • 10.1093/chemse/bjh002
  • 10.3390/nu12041195
 Nomura K, Nakanishi M, Ishidate F, Iwata K, Taruno A. All-Electrical Ca2+-Independent Signal Transduction Mediates Attractive Sodium Taste in Taste Buds. Neuron. 2020 Jun 03;106(5):816–829.e6. doi: 10.1016/j.neuron.2020.03.006. PMID: 32229307.; Bigiani A. Does ENaC Work as Sodium Taste Receptor in Humans? Nutrients. 2020 Apr 24;12(4). PMID: 32344597; PMCID: PMC7230849.; Lossow K, Hermans-Borgmeyer I, Meyerhof W, Behrens M. Segregated Expression of ENaC Subunits in Taste Cells. Chem Senses. 2020 May 21;45(4):235–48. doi: 10.1093/chemse/bjaa004. PMID: 32006019.; Roper SD. The taste of table salt. Pflügers Archiv - European Journal of Physiology. 2015 Jan 07;467(3):457–63. doi: 10.1007/s00424-014-1683-z.; Estacion M, Harty TP, Choi JS, Tyrrell L, Dib-Hajj SD, Waxman SG. A sodium channel gene SCN9A polymorphism that increases nociceptor excitability. Ann Neurol. 2009 Dec;66(6):862–6. doi: 10.1002/ana.21895. PMID: 20033988.; Rossier O, Cao J, Huque T, Spielman AI, Feldman RS, Medrano JF, Brand JG, le Coutre J. Analysis of a human fungiform papillae cDNA library and identification of taste-related genes. Chem Senses. 2004 Jan;29(1):13–23. doi: 10.1093/chemse/bjh002. PMID: 14752036.
Sensory perception of taste

Accession ID: Reactome:R-HSA-9717189
  • 10.1007/s00424-020-02464-4
  • 10.1016/j.neuron.2014.02.022
  • 10.1038/nature08783
  • 10.1038/nrn.2017.68
  • 10.12688/f1000research.21099.1
 Taruno A, Nomura K, Kusakizako T, Ma Z, Nureki O, Foskett JK. Taste transduction and channel synapses in taste buds. Pflügers Archiv - European Journal of Physiology. 2020 Sep 16;473(1):3–13. doi: 10.1007/s00424-020-02464-4.; Kinnamon SC, Finger TE. Recent advances in taste transduction and signaling. F1000Res. 2019 Dec 17;8():2117. doi: 10.12688/f1000research.21099.1.; Roper SD, Chaudhari N. Taste buds: cells, signals and synapses. Nature Reviews Neuroscience. 2017 Jun 29;18(8):485–97. doi: 10.1038/nrn.2017.68.; Liman ER, Zhang YV, Montell C. Peripheral coding of taste. Neuron. 2014 Mar 05;81(5):984–1000. PMID: 24607224; PMCID: PMC3994536.; Chandrashekar J, Kuhn C, Oka Y, Yarmolinsky DA, Hummler E, Ryba NJ, Zuker CS. The cells and peripheral representation of sodium taste in mice. Nature. 2010 Mar 11;464(7286):297–301. PMID: 20107438; PMCID: PMC2849629.
Drug ADME

Accession ID: Reactome:R-BTA-9748784
  • 10.1002/jps.21009
  • 10.2967/jnmt.117.199638
 Currie GM. Pharmacology, Part 2: Introduction to Pharmacokinetics. J Nucl Med Technol. 2018 Sep;46(3):221–30. doi: 10.2967/jnmt.117.199638. PMID: 29724803.; Ruiz-Garcia A, Bermejo M, Moss A, Casabo VG. Pharmacokinetics in Drug Discovery. Journal of Pharmaceutical Sciences. 2008 Feb;97(2):654–90. doi: 10.1002/jps.21009.; Pallasch TJ. Principles of pharmacotherapy: II. Pharmacokinetics. Anesth Prog. 1988 Jul;35(4):133–46. PMID: 3046441; PMCID: PMC2167950.
Azathioprine ADME

Accession ID: Reactome:R-CFA-9748787
  • 10.1016/s1542-3565(04)00344-1
  • 10.1136/gut.39.3.401
  • 10.3389/fphar.2020.582291
  • 10.3748/wjg.v22.i20.4794
 Tominaga K, Sugaya T, Tanaka T, Kanazawa M, Iijima M, Irisawa A. Thiopurines: Recent Topics and Their Role in the Treatment of Inflammatory Bowel Diseases. Front Pharmacol. 2020;11():582291. PMID: 33584261; PMCID: PMC7878672.; Axelrad JE, Lichtiger S, Yajnik V. Inflammatory bowel disease and cancer: The role of inflammation, immunosuppression, and cancer treatment. World J Gastroenterol. 2016 May 28;22(20):4794–801. PMID: 27239106; PMCID: PMC4873872.; Dubinsky MC. Azathioprine, 6-mercaptopurine in inflammatory bowel disease: pharmacology, efficacy, and safety. Clin Gastroenterol Hepatol. 2004 Sep;2(9):731–43. doi: 10.1016/s1542-3565(04)00344-1. PMID: 15354273.; Cuffari C, Théorêt Y, Latour S, Seidman G. 6-Mercaptopurine metabolism in Crohn's disease: correlation with efficacy and toxicity. Gut. 1996 Sep;39(3):401–6. PMID: 8949645; PMCID: PMC1383347.
Drug ADME

Accession ID: Reactome:R-RNO-9748784
  • 10.1002/jps.21009
  • 10.2967/jnmt.117.199638
 Currie GM. Pharmacology, Part 2: Introduction to Pharmacokinetics. J Nucl Med Technol. 2018 Sep;46(3):221–30. doi: 10.2967/jnmt.117.199638. PMID: 29724803.; Ruiz-Garcia A, Bermejo M, Moss A, Casabo VG. Pharmacokinetics in Drug Discovery. Journal of Pharmaceutical Sciences. 2008 Feb;97(2):654–90. doi: 10.1002/jps.21009.; Pallasch TJ. Principles of pharmacotherapy: II. Pharmacokinetics. Anesth Prog. 1988 Jul;35(4):133–46. PMID: 3046441; PMCID: PMC2167950.
Drug ADME

Accession ID: Reactome:R-SSC-9748784
  • 10.1002/jps.21009
  • 10.2967/jnmt.117.199638
 Currie GM. Pharmacology, Part 2: Introduction to Pharmacokinetics. J Nucl Med Technol. 2018 Sep;46(3):221–30. doi: 10.2967/jnmt.117.199638. PMID: 29724803.; Ruiz-Garcia A, Bermejo M, Moss A, Casabo VG. Pharmacokinetics in Drug Discovery. Journal of Pharmaceutical Sciences. 2008 Feb;97(2):654–90. doi: 10.1002/jps.21009.; Pallasch TJ. Principles of pharmacotherapy: II. Pharmacokinetics. Anesth Prog. 1988 Jul;35(4):133–46. PMID: 3046441; PMCID: PMC2167950.