Pathways Knowlegdes
Biological pathway database
| Pathway | DOIs | Note |
|---|---|---|
| GPCR ligand binding Accession ID: Reactome:R-MMU-500792 |
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Kristiansen K. Molecular mechanisms of ligand binding, signaling, and regulation within the superfamily of G-protein-coupled receptors: molecular modeling and mutagenesis approaches to receptor structure and function. Pharmacol Ther. 2004 Jul;103(1):21–80. doi: 10.1016/j.pharmthera.2004.05.002. PMID: 15251227.; Fredriksson R, Lagerström MC, Lundin LG, Schiöth HB. The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints. Mol Pharmacol. 2003 Jun;63(6):1256–72. doi: 10.1124/mol.63.6.1256. PMID: 12761335.; Gether U, Asmar F, Meinild AK, Rasmussen SG. Structural basis for activation of G-protein-coupled receptors. Pharmacol Toxicol. 2002 Dec;91(6):304–12. doi: 10.1034/j.1600-0773.2002.910607.x. PMID: 12688373. |
| Class A/1 (Rhodopsin-like receptors) Accession ID: Reactome:R-RNO-373076 |
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Jacoby E, Bouhelal R, Gerspacher M, Seuwen K. The 7 TM G-protein-coupled receptor target family. ChemMedChem. 2006 Aug;1(8):761–82. doi: 10.1002/cmdc.200600134. PMID: 16902930.; Joost P, Methner A. Phylogenetic analysis of 277 human G-protein-coupled receptors as a tool for the prediction of orphan receptor ligands. Genome Biology. 2002 Oct 17;3(11):research0063.1. doi: 10.1186/gb-2002-3-11-research0063. |
| Organic anion transport by SLC22 transporters Accession ID: Reactome:R-RNO-561048 |
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Ahn S, Bhatnagar V. Update on the molecular physiology of organic anion transporters. Current Opinion in Nephrology and Hypertension. 2008 Sep;17(5):499–505. doi: 10.1097/mnh.0b013e32830b5d5d.; Rizwan AN, Burckhardt G. Organic Anion Transporters of the SLC22 Family: Biopharmaceutical, Physiological, and Pathological Roles. Pharmaceutical Research. 2007 Jan 24;24(3):450–70. doi: 10.1007/s11095-006-9181-4.; Koepsell H, Endou H. The SLC22 drug transporter family. Pflügers Archiv - European Journal of Physiology. 2003 Jul 19;447(5):666–76. doi: 10.1007/s00424-003-1089-9. |
| Transport of small molecules Accession ID: Reactome:R-SSC-382551 |
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| SLC-mediated transmembrane transport Accession ID: Reactome:R-SSC-425407 |
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Schneider S. Inositol transport proteins. FEBS Lett. 2015 Apr 28;589(10):1049–58. doi: 10.1016/j.febslet.2015.03.012. PMID: 25819438.; Anderson CM, Stahl A. SLC27 fatty acid transport proteins. Molecular Aspects of Medicine. 2013 Apr;34(2-3):516–28. doi: 10.1016/j.mam.2012.07.010.; He L, Vasiliou K, Nebert DW. Analysis and update of the human solute carrier (SLC) gene superfamily. Hum Genomics. 2009 Jan;3(2):195–206. PMID: 19164095; PMCID: PMC2752037.; Morris ME, Felmlee MA. Overview of the Proton-coupled MCT (SLC16A) Family of Transporters: Characterization, Function and Role in the Transport of the Drug of Abuse ?-Hydroxybutyric Acid. The AAPS Journal. 2008 Jun 04;10(2):311. doi: 10.1208/s12248-008-9035-6.; Dorwart MR, Shcheynikov N, Yang D, Muallem S. The solute carrier 26 family of proteins in epithelial ion transport. Physiology (Bethesda). 2008 Apr;23():104–14. doi: 10.1152/physiol.00037.2007. PMID: 18400693.; Ashmore J. Cochlear outer hair cell motility. Physiol Rev. 2008 Jan;88(1):173–210. doi: 10.1152/physrev.00044.2006. PMID: 18195086.; Sindic A, Chang MH, Mount DB, Romero MF. Renal physiology of SLC26 anion exchangers. Curr Opin Nephrol Hypertens. 2007 Sep;16(5):484–90. doi: 10.1097/mnh.0b013e3282e7d7d0. PMID: 17693766.; Bressler JP, Olivi L, Cheong JH, Kim Y, Maerten A, Bannon D. Metal transporters in intestine and brain: their involvement in metal-associated neurotoxicities. Hum Exp Toxicol. 2007 Mar;26(3):221–9. doi: 10.1177/0960327107070573. PMID: 17439925.; Handford M, Rodriguez-Furlán C, Orellana A. Nucleotide-sugar transporters: structure, function and roles in vivo. Braz J Med Biol Res. 2006 Sep;39(9):1149–58. doi: 10.1590/s0100-879x2006000900002. PMID: 16981043.; Pajor AM. Molecular properties of the SLC13 family of dicarboxylate and sulfate transporters. Pflügers Archiv - European Journal of Physiology. 2005 Oct 07;451(5):597–605. doi: 10.1007/s00424-005-1487-2.; Traiffort E, Ruat M, O'Regan S, Meunier FM. Molecular characterization of the family of choline transporter-like proteins and their splice variants. Journal of Neurochemistry. 2005 Feb 04;92(5):1116–25. doi: 10.1111/j.1471-4159.2004.02962.x.; Koepsell H, Endou H. The SLC22 drug transporter family. Pflügers Archiv - European Journal of Physiology. 2003 Jul 19;447(5):666–76. doi: 10.1007/s00424-003-1089-9.; Hediger MA, Romero MF, Peng J, Rolfs A, Takanaga H, Bruford EA. The ABCs of solute carriers: physiological, pathological and therapeutic implications of human membrane transport proteins. Pflügers Archiv - European Journal of Physiology. 2003 Nov 18;447(5):465–8. doi: 10.1007/s00424-003-1192-y.; Hagenbuch B, Meier PJ. Organic anion transporting polypeptides of the OATP/ SLC21 family: phylogenetic classification as OATP/ SLCO superfamily, new nomenclature and molecular/functional properties. Pfl?gers Archiv European Journal of Physiology. 2004 Feb 01;447(5):653–65. doi: 10.1007/s00424-003-1168-y.; Chen N, Reith MEA, Quick MW. Synaptic uptake and beyond: the sodium- and chloride-dependent neurotransmitter transporter family SLC6. Pflügers Archiv - European Journal of Physiology. 2003 Apr 29;447(5):519–31. doi: 10.1007/s00424-003-1064-5.; Wood IS, Trayhurn P. Glucose transporters (GLUT and SGLT): expanded families of sugar transport proteins. Br J Nutr. 2003 Jan;89(1):3–9. doi: 10.1079/bjn2002763. PMID: 12568659.; Prasad PD, Wang H, Huang W, Fei YJ, Leibach FH, Devoe LD, Ganapathy V. Molecular and functional characterization of the intestinal Na+-dependent multivitamin transporter. Arch Biochem Biophys. 1999 Jun 01;366(1):95–106. doi: 10.1006/abbi.1999.1213. PMID: 10334869.; Kanamori A, Nakayama J, Fukuda MN, Stallcup WB, Sasaki K, Fukuda M, Hirabayashi Y. Expression cloning and characterization of a cDNA encoding a novel membrane protein required for the formation of O -acetylated ganglioside: A putative acetyl-CoA transporter. Proc. Natl. Acad. Sci. U.S.A. 1997 Apr;94(7):2897–902. doi: 10.1073/pnas.94.7.2897.; Olives B, Neau P, Bailly P, Hediger MA, Rousselet G, Cartron JP, Ripoche P. Cloning and functional expression of a urea transporter from human bone marrow cells. Journal of Biological Chemistry. 1994 Dec;269(50):31649–52. doi: 10.1016/s0021-9258(18)31744-7. |
| Signaling Pathways Accession ID: Reactome:R-SSC-162582 |
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Avraham R, Yarden Y. Feedback regulation of EGFR signalling: decision making by early and delayed loops. Nature Reviews Molecular Cell Biology. 2011 Jan 21;12(2):104–17. doi: 10.1038/nrm3048.; Citi S, Spadaro D, Schneider Y, Stutz J, Pulimeno P. Regulation of small GTPases at epithelial cell-cell junctions. Mol Membr Biol. 2011 Oct;28(7-8):427–44. doi: 10.3109/09687688.2011.603101. PMID: 21781017.; Ritter SL, Hall RA. Fine-tuning of GPCR activity by receptor-interacting proteins. Nature Reviews Molecular Cell Biology. 2009 Dec;10(12):819–30. doi: 10.1038/nrm2803.; Miyazono K, Kamiya Y, Morikawa M. Bone morphogenetic protein receptors and signal transduction. Journal of Biochemistry. 2009 Sep 17;147(1):35–51. doi: 10.1093/jb/mvp148.; Kang JS, Liu C, Derynck R. New regulatory mechanisms of TGF-beta receptor function. Trends Cell Biol. 2009 Aug;19(8):385–94. doi: 10.1016/j.tcb.2009.05.008. PMID: 19648010.; MacDonald BT, Tamai K, He X. Wnt/ß-Catenin Signaling: Components, Mechanisms, and Diseases. Developmental Cell. 2009 Jul;17(1):9–26. doi: 10.1016/j.devcel.2009.06.016.; Angers S, Moon RT. Proximal events in Wnt signal transduction. Nature Reviews Molecular Cell Biology. 2009 Jun 17;10(7):468–77. doi: 10.1038/nrm2717.; Rosenbaum DM, Rasmussen SG, Kobilka BK. The structure and function of G-protein-coupled receptors. Nature. 2009 May 21;459(7245):356–63. PMID: 19458711; PMCID: PMC3967846.; Kopan R, Ilagan MX. The canonical Notch signaling pathway: unfolding the activation mechanism. Cell. 2009 Apr 17;137(2):216–33. PMID: 19379690; PMCID: PMC2827930.; Andrae J, Gallini R, Betsholtz C. Role of platelet-derived growth factors in physiology and medicine. Genes Dev. 2008 May 15;22(10):1276–312. PMID: 18483217; PMCID: PMC2732412.; Oldham WM, Hamm HE. Heterotrimeric G protein activation by G-protein-coupled receptors. Nature Reviews Molecular Cell Biology. 2008 Jan;9(1):60–71. doi: 10.1038/nrm2299.; Manning BD, Cantley LC. AKT/PKB signaling: navigating downstream. Cell. 2007 Jun 29;129(7):1261–74. PMID: 17604717; PMCID: PMC2756685.; McKay MM, Morrison DK. Integrating signals from RTKs to ERK/MAPK. Oncogene. 2007 May 14;26(22):3113–21. doi: 10.1038/sj.onc.1210394. PMID: 17496910.; Hehlgans S, Haase M, Cordes N. Signalling via integrins: Implications for cell survival and anticancer strategies. Biochimica et Biophysica Acta (BBA) - Reviews on Cancer. 2007 Jan;1775(1):163–80. doi: 10.1016/j.bbcan.2006.09.001.; Reichardt LF. Neurotrophin-regulated signalling pathways. Philos Trans R Soc Lond B Biol Sci. 2006 Sep 29;361(1473):1545–64. PMID: 16939974; PMCID: PMC1664664.; Patterson RL, van Rossum DB, Nikolaidis N, Gill DL, Snyder SH. Phospholipase C-gamma: diverse roles in receptor-mediated calcium signaling. Trends Biochem Sci. 2005 Dec;30(12):688–97. doi: 10.1016/j.tibs.2005.10.005. PMID: 16260143.; Eswarakumar VP, Lax I, Schlessinger J. Cellular signaling by fibroblast growth factor receptors. Cytokine Growth Factor Rev. 2005 Apr;16(2):139–49. doi: 10.1016/j.cytogfr.2005.01.001. PMID: 15863030.; Wellbrock C, Karasarides M, Marais R. The RAF proteins take centre stage. Nature Reviews Molecular Cell Biology. 2004 Nov;5(11):875–85. doi: 10.1038/nrm1498.; Xie K, Wei D, Shi Q, Huang S. Constitutive and inducible expression and regulation of vascular endothelial growth factor. Cytokine Growth Factor Rev. 2004 Oct;15(5):297–324. doi: 10.1016/j.cytogfr.2004.04.003. PMID: 15450248.; Saltiel AR, Kahn CR. Insulin signalling and the regulation of glucose and lipid metabolism. Nature. 2001 Dec 13;414(6865):799–806. doi: 10.1038/414799a. PMID: 11742412. |
| Signaling by GPCR Accession ID: Reactome:R-SSC-372790 |
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Oldham WM, Hamm HE. Heterotrimeric G protein activation by G-protein-coupled receptors. Nature Reviews Molecular Cell Biology. 2008 Jan;9(1):60–71. doi: 10.1038/nrm2299.; Jacoby E, Bouhelal R, Gerspacher M, Seuwen K. The 7 TM G-protein-coupled receptor target family. ChemMedChem. 2006 Aug;1(8):761–82. doi: 10.1002/cmdc.200600134. PMID: 16902930.; Bockaert J, Pin JP. Molecular tinkering of G protein-coupled receptors: an evolutionary success. EMBO J. 1999 Apr 01;18(7):1723–9. PMID: 10202136; PMCID: PMC1171258. |
| Proton-coupled monocarboxylate transport Accession ID: Reactome:R-XTR-433692 |
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Merezhinskaya N, Fishbein WN. Monocarboxylate transporters: past, present, and future. Histol Histopathol. 2009 Feb;24(2):243–64. doi: 10.14670/hh-24.243. PMID: 19085840.; Morris ME, Felmlee MA. Overview of the Proton-coupled MCT (SLC16A) Family of Transporters: Characterization, Function and Role in the Transport of the Drug of Abuse ?-Hydroxybutyric Acid. The AAPS Journal. 2008 Jun 04;10(2):311. doi: 10.1208/s12248-008-9035-6.; Wilson MC, Meredith D, Fox JE, Manoharan C, Davies AJ, Halestrap AP. Basigin (CD147) is the target for organomercurial inhibition of monocarboxylate transporter isoforms 1 and 4: the ancillary protein for the insensitive MCT2 is EMBIGIN (gp70). J Biol Chem. 2005 Jul 22;280(29):27213–21. doi: 10.1074/jbc.m411950200. PMID: 15917240. |
| Glycolysis and gluconeogenesis Accession ID: WikiPathways:WP144 |
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| Glycolysis and gluconeogenesis Accession ID: WikiPathways:WP1027 |
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Bricker DK, Taylor EB, Schell JC, Orsak T, Boutron A, Chen Y, Cox JE, Cardon CM, Van Vranken JG, Dephoure N, Redin C, Boudina S, Gygi SP, Brivet M, Thummel CS, Rutter J. A Mitochondrial Pyruvate Carrier Required for Pyruvate Uptake in Yeast, Drosophila , and Humans. Science. 2012 Jul 06;337(6090):96–100. doi: 10.1126/science.1218099. |
| HIF1A and PPARG regulation of glycolysis Accession ID: WikiPathways:WP2456 |
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| Biochemical pathways: part I Accession ID: WikiPathways:WP3604 |
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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. |
| AtMetExpress overview Accession ID: WikiPathways:WP3622 |
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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. |
| Metabolic Epileptic Disorders Accession ID: WikiPathways:WP5355 |
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Tan M, Mosaoa R, Graham GT, Kasprzyk-Pawelec A, Gadre S, Parasido E, Catalina-Rodriguez O, Foley P, Giaccone G, Cheema A, Kallakury B, Albanese C, Yi C, Avantaggiati ML. Inhibition of the mitochondrial citrate carrier, Slc25a1, reverts steatosis, glucose intolerance, and inflammation in preclinical models of NAFLD/NASH. Cell Death & Differentiation. 2020 Jan 20;27(7):2143–57. doi: 10.1038/s41418-020-0491-6. |
| TCA cycle nutrient use and invasiveness of ovarian cancer Accession ID: WikiPathways:WP2868 |
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Yang L, Moss T, Mangala LS, Marini J, Zhao H, Wahlig S, Armaiz-Pena G, Jiang D, Achreja A, Win J, Roopaimoole R, Rodriguez-Aguayo C, Mercado-Uribe I, Lopez-Berestein G, Liu J, Tsukamoto T, Sood AK, Ram PT, Nagrath D. Metabolic shifts toward glutamine regulate tumor growth, invasion and bioenergetics in ovarian cancer. Mol Syst Biol. 2014 May 05;10():728. PMID: 24799285; PMCID: PMC4188042. |
| Amino acid metabolism Accession ID: WikiPathways:WP662 |
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| Metabolic pathways of fibroblasts Accession ID: WikiPathways:WP5312 |
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Rabinowitz JD, Mutlu GM. A metabolic strategy to reverse fibrosis? Nat Metab. 2019 Jan;1(1):12–3. doi: 10.1038/s42255-018-0013-8. PMID: 32694811. |
| TCA cycle nutrient use and invasiveness of ovarian cancer Accession ID: WikiPathways:WP3252 |
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Yang L, Moss T, Mangala LS, Marini J, Zhao H, Wahlig S, Armaiz-Pena G, Jiang D, Achreja A, Win J, Roopaimoole R, Rodriguez-Aguayo C, Mercado-Uribe I, Lopez-Berestein G, Liu J, Tsukamoto T, Sood AK, Ram PT, Nagrath D. Metabolic shifts toward glutamine regulate tumor growth, invasion and bioenergetics in ovarian cancer. Mol Syst Biol. 2014 May 05;10():728. PMID: 24799285; PMCID: PMC4188042. |
| NAD+ metabolism Accession ID: WikiPathways:WP3644 |
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Verdin E. NAD? in aging, metabolism, and neurodegeneration. Science. 2015 Dec 04;350(6265):1208–13. doi: 10.1126/science.aac4854. PMID: 26785480. |
| Glucose homeostasis Accession ID: WikiPathways:WP661 |
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Shaham O, Wei R, Wang TJ, Ricciardi C, Lewis GD, Vasan RS, Carr SA, Thadhani R, Gerszten RE, Mootha VK. Metabolic profiling of the human response to a glucose challenge reveals distinct axes of insulin sensitivity. Molecular Systems Biology. 2008 Jan;4(1). doi: 10.1038/msb.2008.50. |