Pathways Knowlegdes

Biological pathway database

Pathway DOIs Note
PCO cycle

Accession ID: Plant Reactome:R-ORU-1119312
  • 10.1016/j.jphotobiol.2014.11.009
  • 10.1016/j.molp.2016.02.002
  • 10.1093/jxb/erp056
  • 10.1093/jxb/erq028
  • 10.1093/jxb/ers398
  • 10.1104/pp.106.085514
  • 10.1104/pp.112.201459
  • 10.1111/j.1365-3040.2009.01937.x
  • 10.1111/j.1438-8677.2012.00723.x
  • 10.1111/jipb.12125
  • 10.1111/jipb.12336
  • 10.1111/pce.12078
  • 10.1111/ppl.12104
  • 10.1371/journal.pone.0039658
  • 10.3389/fpls.2016.01165
  • 10.7717/peerj.28
 Cui LL, Lu YS, Li Y, Yang C, Peng XX. Overexpression of Glycolate Oxidase Confers Improved Photosynthesis under High Light and High Temperature in Rice. Front Plant Sci. 2016;7():1165. PMID: 27540387; PMCID: PMC4972838.; Zhang Z, Xu Y, Xie Z, Li X, He ZH, Peng XX. Association-Dissociation of Glycolate Oxidase with Catalase in Rice: A Potential Switch to Modulate Intracellular H2O2 Levels. Mol Plant. 2016 May 02;9(5):737–48. doi: 10.1016/j.molp.2016.02.002. PMID: 26900141.; Wang D, Liu H, Li S, Zhai G, Shao J, Tao Y. Characterization and molecular cloning of a serine hydroxymethyltransferase 1 (OsSHM1) in rice. J Integr Plant Biol. 2015 Sep;57(9):745–56. doi: 10.1111/jipb.12336. PMID: 25641188.; Zhang Z, Mao X, Ou J, Ye N, Zhang J, Peng X. Distinct photorespiratory reactions are preferentially catalyzed by glutamate:glyoxylate and serine:glyoxylate aminotransferases in rice. Journal of Photochemistry and Photobiology B: Biology. 2015 Jan;142():110–7. doi: 10.1016/j.jphotobiol.2014.11.009.; Ye N, Yang G, Chen Y, Zhang C, Zhang J, Peng X. Two hydroxypyruvate reductases encoded by OsHPR1 and OsHPR2 are involved in photorespiratory metabolism in rice. J Integr Plant Biol. 2014 Feb;56(2):170–80. doi: 10.1111/jipb.12125. PMID: 24401104.; Lu Y, Li Y, Yang Q, Zhang Z, Chen Y, Zhang S, Peng XX. Suppression of glycolate oxidase causes glyoxylate accumulation that inhibits photosynthesis through deactivating Rubisco in rice. Physiol Plant. 2014 Mar;150(3):463–76. doi: 10.1111/ppl.12104. PMID: 24102419.; Sørhagen K, Laxa M, Peterhänsel C, Reumann S. The emerging role of photorespiration and non-photorespiratory peroxisomal metabolism in pathogen defence. Plant Biol (Stuttg). 2013 Jul;15(4):723–36. doi: 10.1111/j.1438-8677.2012.00723.x. PMID: 23506300.; ZHOU Q, YU Q, WANG Z, PAN Y, LV W, ZHU L, CHEN R, HE G. Knockdown of GDCH gene reveals reactive oxygen species-induced leaf senescence in rice. Plant Cell & Environment. 2013 Mar 12;36(8):1476–89. doi: 10.1111/pce.12078.; Chern M, Bai W, Chen X, Canlas PE, Ronald PC. Reduced expression of glycolate oxidase leads to enhanced disease resistance in rice. PeerJ. 2013;1():e28. PMID: 23638363; PMCID: PMC3628735.; Suzuki Y, Makino A. Translational downregulation of RBCL is operative in the coordinated expression of Rubisco genes in senescent leaves in rice. J Exp Bot. 2013 Feb;64(4):1145–52. PMID: 23349140; PMCID: PMC3580822.; Suzuki Y, Makino A. Availability of Rubisco small subunit up-regulates the transcript levels of large subunit for stoichiometric assembly of its holoenzyme in rice. Plant Physiol. 2012 Sep;160(1):533–40. PMID: 22811433; PMCID: PMC3440226.; Zhang Z, Lu Y, Zhai L, Deng R, Jiang J, Li Y, He Z, Peng X. Glycolate Oxidase Isozymes Are Coordinately Controlled by GLO1 and GLO4 in Rice. PLoS ONE. 2012 Jun 26;7(6):e39658. doi: 10.1371/journal.pone.0039658.; Yu L, Jiang J, Zhang C, Jiang L, Ye N, Lu Y, Yang G, Liu E, Peng C, He Z, Peng X. Glyoxylate rather than ascorbate is an efficient precursor for oxalate biosynthesis in rice. J Exp Bot. 2010 Jun;61(6):1625–34. PMID: 20194922; PMCID: PMC2914580.; Xu H, Zhang J, Zeng J, Jiang L, Liu E, Peng C, He Z, Peng X. Inducible antisense suppression of glycolate oxidase reveals its strong regulation over photosynthesis in rice. J Exp Bot. 2009;60(6):1799–809. doi: 10.1093/jxb/erp056. PMID: 19264754.; SUZUKI Y, MIYAMOTO T, YOSHIZAWA R, MAE T, MAKINO A. Rubisco content and photosynthesis of leaves at different positions in transgenic rice with an overexpression of RBCS. Plant Cell & Environment. 2009 Mar 05;32(4):417–27. doi: 10.1111/j.1365-3040.2009.01937.x.; Igarashi D, Tsuchida H, Miyao M, Ohsumi C. Glutamate:glyoxylate aminotransferase modulates amino acid content during photorespiration. Plant Physiol. 2006 Nov;142(3):901–10. PMID: 16950862; PMCID: PMC1630728.
Metabolism and regulation

Accession ID: Plant Reactome:R-TCA-2744345		 -
Metabolism and regulation

Accession ID: Plant Reactome:R-OSI-2744345		 -
Oxidative stress and redox pathway

Accession ID: WikiPathways:WP4466
  • 10.1074/jbc.m110.189944
 Yan Z, Garg SK, Banerjee R. Regulatory T Cells Interfere with Glutathione Metabolism in Dendritic Cells and T Cells. Journal of Biological Chemistry. 2010 Dec;285(53):41525–32. doi: 10.1074/jbc.m110.189944.
Dravet syndrome: Scn1a-A1783V point mutation model

Accession ID: WikiPathways:WP5298
  • 10.1016/j.neuron.2007.04.001
 Wierda KD, Toonen RF, de Wit H, Brussaard AB, Verhage M. Interdependence of PKC-dependent and PKC-independent pathways for presynaptic plasticity. Neuron. 2007 Apr 19;54(2):275–90. doi: 10.1016/j.neuron.2007.04.001. PMID: 17442248.
Folic acid network

Accession ID: WikiPathways:WP1311
  • 10.1016/j.febslet.2006.08.065
 Lu C, Qiu F, Zhou H, Peng Y, Hao W, Xu J, Yuan J, Wang S, Qiang B, Xu C, Peng X. Identification and characterization of selenoprotein K: an antioxidant in cardiomyocytes. FEBS Lett. 2006 Oct 02;580(22):5189–97. doi: 10.1016/j.febslet.2006.08.065. PMID: 16962588.
Tyrosine biosynthesis

Accession ID: WikiPathways:WP538
  • 10.1007/s004380050643
 Urrestarazu A, Vissers S, Iraqui I, Grenson M. Phenylalanine- and tyrosine-auxotrophic mutants of Saccharomyces cerevisiae impaired in transamination. Molecular Genetics and Genomics. 1998 Jan;257(2):230–7. doi: 10.1007/s004380050643.
Cadmium and glutathione

Accession ID: WikiPathways:WP2579
  • 10.1016/j.plaphy.2014.07.001
 Jozefczak M, Keunen E, Schat H, Bliek M, Hernández LE, Carleer R, Remans T, Bohler S, Vangronsveld J, Cuypers A. Differential response of Arabidopsis leaves and roots to cadmium: glutathione-related chelating capacity vs antioxidant capacity. Plant Physiol Biochem. 2014 Oct;83():1–9. doi: 10.1016/j.plaphy.2014.07.001. PMID: 25049163.
Biogenic amine synthesis

Accession ID: WikiPathways:WP522		 -
Glutathione and one-carbon metabolism

Accession ID: WikiPathways:WP730
  • 10.1093/carcin/bgm062
 Hazra A, Wu K, Kraft P, Fuchs CS, Giovannucci EL, Hunter DJ. Twenty-four non-synonymous polymorphisms in the one-carbon metabolic pathway and risk of colorectal adenoma in the Nurses' Health Study. Carcinogenesis. 2007 Jul;28(7):1510–9. doi: 10.1093/carcin/bgm062. PMID: 17389618.
Amino acid transport defects (IEMs)

Accession ID: WikiPathways:WP5029
  • 10.1523/jneurosci.14-09-05559.1994
 Arriza J, Fairman W, Wadiche J, Murdoch G, Kavanaugh M, Amara S. Functional comparisons of three glutamate transporter subtypes cloned from human motor cortex. J. Neurosci. 1994 Sep 01;14(9):5559–69. doi: 10.1523/jneurosci.14-09-05559.1994.
NAD biosynthesis II from tryptophan

Accession ID: WikiPathways:WP3228		 -
Amyotrophic lateral sclerosis (ALS)

Accession ID: WikiPathways:WP3243
  • 10.1016/j.neulet.2011.04.047
 Flomen R, Makoff A. Increased RNA editing in EAAT2 pre-mRNA from amyotrophic lateral sclerosis patients: involvement of a cryptic polyadenylation site. Neurosci Lett. 2011 Jun 22;497(2):139–43. doi: 10.1016/j.neulet.2011.04.047. PMID: 21569822.
Glutathione metabolism

Accession ID: WikiPathways:WP100		 -
Biochemical pathways: part I

Accession ID: WikiPathways:WP3604
  • 10.1016/s0303-2647(98)00019-7
 Michal G. On representation of metabolic pathways. Biosystems. 1998 Jun;47(1-2):1–7. doi: 10.1016/s0303-2647(98)00019-7. PMID: 9715748.
Amino acid metabolism pathway excerpt: histidine catabolism extension

Accession ID: WikiPathways:WP4661		 -
Orexin receptor pathway

Accession ID: WikiPathways:WP5094
  • 10.1210/jc.86.9.4512
 Karteris E, Randeva HS, Grammatopoulos DK, Jaffe RB, Hillhouse EW. Expression and Coupling Characteristics of the CRH and Orexin Type 2 Receptors in Human Fetal Adrenals. The Journal of Clinical Endocrinology & Metabolism. 2001 Sep;86(9):4512–9. doi: 10.1210/jcem.86.9.7849.
Amino acid metabolism in triple-negative breast cancer cells

Accession ID: WikiPathways:WP5213
  • 10.1158/0008-5472.can-14-3745
 Bhutia YD, Babu E, Ramachandran S, Ganapathy V. Amino Acid transporters in cancer and their relevance to 'glutamine addiction': novel targets for the design of a new class of anticancer drugs. Cancer Res. 2015 May 01;75(9):1782–8. doi: 10.1158/0008-5472.can-14-3745. PMID: 25855379.
AtMetExpress overview

Accession ID: WikiPathways:WP3622
  • 10.1039/c4np00072b
 Sumner LW, Lei Z, Nikolau BJ, Saito K. Modern plant metabolomics: advanced natural product gene discoveries, improved technologies, and future prospects. Nat Prod Rep. 2015 Feb;32(2):212–29. doi: 10.1039/c4np00072b. PMID: 25342293.
Glutathione metabolism

Accession ID: WikiPathways:WP164		 -