Pathways Knowlegdes

Biological pathway database

Pathway DOIs Note
Signaling by Retinoic Acid

Accession ID: Reactome:R-SSC-5362517
  • 10.1016/j.bbalip.2011.05.004
  • 10.1016/j.bbalip.2011.06.002
  • 10.1016/j.bmc.2013.11.025
  • 10.1146/annurev-nutr-072610-145127
 Das BC, Thapa P, Karki R, Das S, Mahapatra S, Liu T, Torregroza I, Wallace DP, Kambhampati S, Van Veldhuizen P, Verma A, Ray SK, Evans T. Retinoic acid signaling pathways in development and diseases. Bioorganic & Medicinal Chemistry. 2014 Jan;22(2):673–83. doi: 10.1016/j.bmc.2013.11.025.; Harrison EH. Mechanisms involved in the intestinal absorption of dietary vitamin A and provitamin A carotenoids. Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids. 2012 Jan;1821(1):70–7. doi: 10.1016/j.bbalip.2011.06.002.; Napoli JL. Physiological insights into all-trans-retinoic acid biosynthesis. Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids. 2012 Jan;1821(1):152–67. doi: 10.1016/j.bbalip.2011.05.004.; Catharine Ross A, Zolfaghari R. Cytochrome P450s in the Regulation of Cellular Retinoic Acid Metabolism. Annu. Rev. Nutr. 2011 Aug 21;31(1):65–87. doi: 10.1146/annurev-nutr-072610-145127.
Visual phototransduction

Accession ID: Reactome:R-XTR-2187338
  • 10.1002/neu.20242
  • 10.1016/0005-2728(93)90038-h
  • 10.1016/j.preteyeres.2010.11.001
  • 10.1016/j.preteyeres.2012.05.002
  • 10.1016/j.tibs.2010.01.005
  • 10.1074/jbc.r111.303008
  • 10.1074/jbc.r111.303990
  • 10.1093/jn/131.5.1405
  • 10.1111/j.1753-4887.2004.tb00053.x
  • 10.1146/annurev.nutr.25.050304.092614
  • 10.1152/physiol.00001.2010
  • 10.3390/nu3010063
 Korenbrot JI. Speed, sensitivity, and stability of the light response in rod and cone photoreceptors: Facts and models. Progress in Retinal and Eye Research. 2012 Sep;31(5):442–66. doi: 10.1016/j.preteyeres.2012.05.002.; von Lintig J. Metabolism of Carotenoids and Retinoids Related to Vision. Journal of Biological Chemistry. 2012 Jan;287(3):1627–34. doi: 10.1074/jbc.r111.303990.; Kefalov VJ. Rod and Cone Visual Pigments and Phototransduction through Pharmacological, Genetic, and Physiological Approaches. Journal of Biological Chemistry. 2012 Jan;287(3):1635–41. doi: 10.1074/jbc.r111.303008.; Wang J, Kefalov VJ. The Cone-specific visual cycle. Progress in Retinal and Eye Research. 2011 Mar;30(2):115–28. doi: 10.1016/j.preteyeres.2010.11.001.; D'Ambrosio DN, Clugston RD, Blaner WS. Vitamin A metabolism: an update. Nutrients. 2011 Jan;3(1):63–103. PMID: 21350678; PMCID: PMC3042718.; von Lintig J, Kiser PD, Golczak M, Palczewski K. The biochemical and structural basis for trans-to-cis isomerization of retinoids in the chemistry of vision. Trends in Biochemical Sciences. 2010 Jul;35(7):400–10. doi: 10.1016/j.tibs.2010.01.005.; Burns ME, Pugh EN. Lessons from photoreceptors: turning off g-protein signaling in living cells. Physiology (Bethesda). 2010 Apr;25(2):72–84. PMID: 20430952; PMCID: PMC2880230.; Blomhoff R, Blomhoff HK. Overview of retinoid metabolism and function. J Neurobiol. 2006 Jun;66(7):606–30. doi: 10.1002/neu.20242. PMID: 16688755.; Harrison EH. Mechanisms of digestion and absorption of dietary vitamin A. Annu Rev Nutr. 2005;25():87–103. doi: 10.1146/annurev.nutr.25.050304.092614. PMID: 16011460.; Wolf G. The visual cycle of the cone photoreceptors of the retina. Nutr Rev. 2004 Jul;62(7 Pt 1):283–6. doi: 10.1111/j.1753-4887.2004.tb00053.x. PMID: 15384919.; Harrison EH, Hussain MM. Mechanisms Involved in the Intestinal Digestion and Absorption of Dietary Vitamin A. The Journal of Nutrition. 2001 May;131(5):1405–8. doi: 10.1093/jn/131.5.1405.; Pugh EN, Lamb TD. Amplification and kinetics of the activation steps in phototransduction. Biochimica et Biophysica Acta (BBA) - Bioenergetics. 1993 Mar;1141(2-3):111–49. doi: 10.1016/0005-2728(93)90038-h.
Signaling by Nuclear Receptors

Accession ID: Reactome:R-XTR-9006931
  • 10.1016/0039-128x(96)00030-x
  • 10.1016/bs.ctdb.2017.02.003
  • 10.1016/j.bbamcr.2009.11.012
  • 10.1016/j.bbamcr.2016.06.004
  • 10.1016/j.mce.2013.06.021
  • 10.1038/nrm.2016.122
  • 10.1210/me.2013-1334
 Holzer G, Markov GV, Laudet V. Evolution of Nuclear Receptors and Ligand Signaling: Toward a Soft Key-Lock Model? Curr Top Dev Biol. 2017;125():1–38. doi: 10.1016/bs.ctdb.2017.02.003. PMID: 28527568.; Levin ER, Hammes SR. Nuclear receptors outside the nucleus: extranuclear signalling by steroid receptors. Nature Reviews Molecular Cell Biology. 2016 Oct 12;17(12):783–97. doi: 10.1038/nrm.2016.122.; Schwartz N, Verma A, Bivens CB, Schwartz Z, Boyan BD. Rapid steroid hormone actions via membrane receptors. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research. 2016 Sep;1863(9):2289–98. doi: 10.1016/j.bbamcr.2016.06.004.; Simons SS, Edwards DP, Kumar R. Minireview: dynamic structures of nuclear hormone receptors: new promises and challenges. Mol Endocrinol. 2014 Feb;28(2):173–82. PMID: 24284822; PMCID: PMC3896641.; Hah N, Kraus WL. Hormone-regulated transcriptomes: Lessons learned from estrogen signaling pathways in breast cancer cells. Molecular and Cellular Endocrinology. 2014 Jan;382(1):652–64. doi: 10.1016/j.mce.2013.06.021.; Echeverria PC, Picard D. Molecular chaperones, essential partners of steroid hormone receptors for activity and mobility. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research. 2010 Jun;1803(6):641–9. doi: 10.1016/j.bbamcr.2009.11.012.; Beato M, Chávez S, Truss M. Transcriptional regulation by steroid hormones. Steroids. 1996 Apr;61(4):240–51. doi: 10.1016/0039-128x(96)00030-x. PMID: 8733009.
The retinoid cycle in cones (daylight vision)

Accession ID: Reactome:R-BTA-2187335
  • 10.1016/j.preteyeres.2010.11.001
  • 10.1074/jbc.r111.303008
  • 10.1074/jbc.r111.303990
  • 10.1111/j.1753-4887.2004.tb00053.x
 von Lintig J. Metabolism of Carotenoids and Retinoids Related to Vision. Journal of Biological Chemistry. 2012 Jan;287(3):1627–34. doi: 10.1074/jbc.r111.303990.; Kefalov VJ. Rod and Cone Visual Pigments and Phototransduction through Pharmacological, Genetic, and Physiological Approaches. Journal of Biological Chemistry. 2012 Jan;287(3):1635–41. doi: 10.1074/jbc.r111.303008.; Wang J, Kefalov VJ. The Cone-specific visual cycle. Progress in Retinal and Eye Research. 2011 Mar;30(2):115–28. doi: 10.1016/j.preteyeres.2010.11.001.; Wolf G. The visual cycle of the cone photoreceptors of the retina. Nutr Rev. 2004 Jul;62(7 Pt 1):283–6. doi: 10.1111/j.1753-4887.2004.tb00053.x. PMID: 15384919.
Signaling by Nuclear Receptors

Accession ID: Reactome:R-BTA-9006931
  • 10.1016/0039-128x(96)00030-x
  • 10.1016/bs.ctdb.2017.02.003
  • 10.1016/j.bbamcr.2009.11.012
  • 10.1016/j.bbamcr.2016.06.004
  • 10.1016/j.mce.2013.06.021
  • 10.1038/nrm.2016.122
  • 10.1210/me.2013-1334
 Holzer G, Markov GV, Laudet V. Evolution of Nuclear Receptors and Ligand Signaling: Toward a Soft Key-Lock Model? Curr Top Dev Biol. 2017;125():1–38. doi: 10.1016/bs.ctdb.2017.02.003. PMID: 28527568.; Levin ER, Hammes SR. Nuclear receptors outside the nucleus: extranuclear signalling by steroid receptors. Nature Reviews Molecular Cell Biology. 2016 Oct 12;17(12):783–97. doi: 10.1038/nrm.2016.122.; Schwartz N, Verma A, Bivens CB, Schwartz Z, Boyan BD. Rapid steroid hormone actions via membrane receptors. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research. 2016 Sep;1863(9):2289–98. doi: 10.1016/j.bbamcr.2016.06.004.; Simons SS, Edwards DP, Kumar R. Minireview: dynamic structures of nuclear hormone receptors: new promises and challenges. Mol Endocrinol. 2014 Feb;28(2):173–82. PMID: 24284822; PMCID: PMC3896641.; Hah N, Kraus WL. Hormone-regulated transcriptomes: Lessons learned from estrogen signaling pathways in breast cancer cells. Molecular and Cellular Endocrinology. 2014 Jan;382(1):652–64. doi: 10.1016/j.mce.2013.06.021.; Echeverria PC, Picard D. Molecular chaperones, essential partners of steroid hormone receptors for activity and mobility. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research. 2010 Jun;1803(6):641–9. doi: 10.1016/j.bbamcr.2009.11.012.; Beato M, Chávez S, Truss M. Transcriptional regulation by steroid hormones. Steroids. 1996 Apr;61(4):240–51. doi: 10.1016/0039-128x(96)00030-x. PMID: 8733009.
The canonical retinoid cycle in rods (twilight vision)

Accession ID: Reactome:R-CEL-2453902
  • 10.1002/neu.20242
  • 10.1016/j.tibs.2010.01.005
  • 10.1074/jbc.r111.303990
  • 10.3390/nu3010063
 von Lintig J. Metabolism of Carotenoids and Retinoids Related to Vision. Journal of Biological Chemistry. 2012 Jan;287(3):1627–34. doi: 10.1074/jbc.r111.303990.; D'Ambrosio DN, Clugston RD, Blaner WS. Vitamin A metabolism: an update. Nutrients. 2011 Jan;3(1):63–103. PMID: 21350678; PMCID: PMC3042718.; von Lintig J, Kiser PD, Golczak M, Palczewski K. The biochemical and structural basis for trans-to-cis isomerization of retinoids in the chemistry of vision. Trends in Biochemical Sciences. 2010 Jul;35(7):400–10. doi: 10.1016/j.tibs.2010.01.005.; Blomhoff R, Blomhoff HK. Overview of retinoid metabolism and function. J Neurobiol. 2006 Jun;66(7):606–30. doi: 10.1002/neu.20242. PMID: 16688755.
RA biosynthesis pathway

Accession ID: Reactome:R-CFA-5365859
  • 10.1016/j.bbalip.2011.05.004
  • 10.1016/j.bmc.2013.11.025
 Das BC, Thapa P, Karki R, Das S, Mahapatra S, Liu T, Torregroza I, Wallace DP, Kambhampati S, Van Veldhuizen P, Verma A, Ray SK, Evans T. Retinoic acid signaling pathways in development and diseases. Bioorganic & Medicinal Chemistry. 2014 Jan;22(2):673–83. doi: 10.1016/j.bmc.2013.11.025.; Napoli JL. Physiological insights into all-trans-retinoic acid biosynthesis. Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids. 2012 Jan;1821(1):152–67. doi: 10.1016/j.bbalip.2011.05.004.
Visual phototransduction

Accession ID: Reactome:R-DRE-2187338
  • 10.1002/neu.20242
  • 10.1016/0005-2728(93)90038-h
  • 10.1016/j.preteyeres.2010.11.001
  • 10.1016/j.preteyeres.2012.05.002
  • 10.1016/j.tibs.2010.01.005
  • 10.1074/jbc.r111.303008
  • 10.1074/jbc.r111.303990
  • 10.1093/jn/131.5.1405
  • 10.1111/j.1753-4887.2004.tb00053.x
  • 10.1146/annurev.nutr.25.050304.092614
  • 10.1152/physiol.00001.2010
  • 10.3390/nu3010063
 Korenbrot JI. Speed, sensitivity, and stability of the light response in rod and cone photoreceptors: Facts and models. Progress in Retinal and Eye Research. 2012 Sep;31(5):442–66. doi: 10.1016/j.preteyeres.2012.05.002.; von Lintig J. Metabolism of Carotenoids and Retinoids Related to Vision. Journal of Biological Chemistry. 2012 Jan;287(3):1627–34. doi: 10.1074/jbc.r111.303990.; Kefalov VJ. Rod and Cone Visual Pigments and Phototransduction through Pharmacological, Genetic, and Physiological Approaches. Journal of Biological Chemistry. 2012 Jan;287(3):1635–41. doi: 10.1074/jbc.r111.303008.; Wang J, Kefalov VJ. The Cone-specific visual cycle. Progress in Retinal and Eye Research. 2011 Mar;30(2):115–28. doi: 10.1016/j.preteyeres.2010.11.001.; D'Ambrosio DN, Clugston RD, Blaner WS. Vitamin A metabolism: an update. Nutrients. 2011 Jan;3(1):63–103. PMID: 21350678; PMCID: PMC3042718.; von Lintig J, Kiser PD, Golczak M, Palczewski K. The biochemical and structural basis for trans-to-cis isomerization of retinoids in the chemistry of vision. Trends in Biochemical Sciences. 2010 Jul;35(7):400–10. doi: 10.1016/j.tibs.2010.01.005.; Burns ME, Pugh EN. Lessons from photoreceptors: turning off g-protein signaling in living cells. Physiology (Bethesda). 2010 Apr;25(2):72–84. PMID: 20430952; PMCID: PMC2880230.; Blomhoff R, Blomhoff HK. Overview of retinoid metabolism and function. J Neurobiol. 2006 Jun;66(7):606–30. doi: 10.1002/neu.20242. PMID: 16688755.; Harrison EH. Mechanisms of digestion and absorption of dietary vitamin A. Annu Rev Nutr. 2005;25():87–103. doi: 10.1146/annurev.nutr.25.050304.092614. PMID: 16011460.; Wolf G. The visual cycle of the cone photoreceptors of the retina. Nutr Rev. 2004 Jul;62(7 Pt 1):283–6. doi: 10.1111/j.1753-4887.2004.tb00053.x. PMID: 15384919.; Harrison EH, Hussain MM. Mechanisms Involved in the Intestinal Digestion and Absorption of Dietary Vitamin A. The Journal of Nutrition. 2001 May;131(5):1405–8. doi: 10.1093/jn/131.5.1405.; Pugh EN, Lamb TD. Amplification and kinetics of the activation steps in phototransduction. Biochimica et Biophysica Acta (BBA) - Bioenergetics. 1993 Mar;1141(2-3):111–49. doi: 10.1016/0005-2728(93)90038-h.
The canonical retinoid cycle in rods (twilight vision)

Accession ID: Reactome:R-DME-2453902
  • 10.1002/neu.20242
  • 10.1016/j.tibs.2010.01.005
  • 10.1074/jbc.r111.303990
  • 10.3390/nu3010063
 von Lintig J. Metabolism of Carotenoids and Retinoids Related to Vision. Journal of Biological Chemistry. 2012 Jan;287(3):1627–34. doi: 10.1074/jbc.r111.303990.; D'Ambrosio DN, Clugston RD, Blaner WS. Vitamin A metabolism: an update. Nutrients. 2011 Jan;3(1):63–103. PMID: 21350678; PMCID: PMC3042718.; von Lintig J, Kiser PD, Golczak M, Palczewski K. The biochemical and structural basis for trans-to-cis isomerization of retinoids in the chemistry of vision. Trends in Biochemical Sciences. 2010 Jul;35(7):400–10. doi: 10.1016/j.tibs.2010.01.005.; Blomhoff R, Blomhoff HK. Overview of retinoid metabolism and function. J Neurobiol. 2006 Jun;66(7):606–30. doi: 10.1002/neu.20242. PMID: 16688755.
Signaling by Retinoic Acid

Accession ID: Reactome:R-DME-5362517
  • 10.1016/j.bbalip.2011.05.004
  • 10.1016/j.bbalip.2011.06.002
  • 10.1016/j.bmc.2013.11.025
  • 10.1146/annurev-nutr-072610-145127
 Das BC, Thapa P, Karki R, Das S, Mahapatra S, Liu T, Torregroza I, Wallace DP, Kambhampati S, Van Veldhuizen P, Verma A, Ray SK, Evans T. Retinoic acid signaling pathways in development and diseases. Bioorganic & Medicinal Chemistry. 2014 Jan;22(2):673–83. doi: 10.1016/j.bmc.2013.11.025.; Harrison EH. Mechanisms involved in the intestinal absorption of dietary vitamin A and provitamin A carotenoids. Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids. 2012 Jan;1821(1):70–7. doi: 10.1016/j.bbalip.2011.06.002.; Napoli JL. Physiological insights into all-trans-retinoic acid biosynthesis. Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids. 2012 Jan;1821(1):152–67. doi: 10.1016/j.bbalip.2011.05.004.; Catharine Ross A, Zolfaghari R. Cytochrome P450s in the Regulation of Cellular Retinoic Acid Metabolism. Annu. Rev. Nutr. 2011 Aug 21;31(1):65–87. doi: 10.1146/annurev-nutr-072610-145127.
RA biosynthesis pathway

Accession ID: Reactome:R-GGA-5365859
  • 10.1016/j.bbalip.2011.05.004
  • 10.1016/j.bmc.2013.11.025
 Das BC, Thapa P, Karki R, Das S, Mahapatra S, Liu T, Torregroza I, Wallace DP, Kambhampati S, Van Veldhuizen P, Verma A, Ray SK, Evans T. Retinoic acid signaling pathways in development and diseases. Bioorganic & Medicinal Chemistry. 2014 Jan;22(2):673–83. doi: 10.1016/j.bmc.2013.11.025.; Napoli JL. Physiological insights into all-trans-retinoic acid biosynthesis. Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids. 2012 Jan;1821(1):152–67. doi: 10.1016/j.bbalip.2011.05.004.
Visual phototransduction

Accession ID: Reactome:R-HSA-2187338
  • 10.1002/neu.20242
  • 10.1016/0005-2728(93)90038-h
  • 10.1016/j.preteyeres.2010.11.001
  • 10.1016/j.preteyeres.2012.05.002
  • 10.1016/j.tibs.2010.01.005
  • 10.1074/jbc.r111.303008
  • 10.1074/jbc.r111.303990
  • 10.1093/jn/131.5.1405
  • 10.1111/j.1753-4887.2004.tb00053.x
  • 10.1146/annurev.nutr.25.050304.092614
  • 10.1152/physiol.00001.2010
  • 10.3390/nu3010063
 Korenbrot JI. Speed, sensitivity, and stability of the light response in rod and cone photoreceptors: Facts and models. Progress in Retinal and Eye Research. 2012 Sep;31(5):442–66. doi: 10.1016/j.preteyeres.2012.05.002.; von Lintig J. Metabolism of Carotenoids and Retinoids Related to Vision. Journal of Biological Chemistry. 2012 Jan;287(3):1627–34. doi: 10.1074/jbc.r111.303990.; Kefalov VJ. Rod and Cone Visual Pigments and Phototransduction through Pharmacological, Genetic, and Physiological Approaches. Journal of Biological Chemistry. 2012 Jan;287(3):1635–41. doi: 10.1074/jbc.r111.303008.; Wang J, Kefalov VJ. The Cone-specific visual cycle. Progress in Retinal and Eye Research. 2011 Mar;30(2):115–28. doi: 10.1016/j.preteyeres.2010.11.001.; D'Ambrosio DN, Clugston RD, Blaner WS. Vitamin A metabolism: an update. Nutrients. 2011 Jan;3(1):63–103. PMID: 21350678; PMCID: PMC3042718.; von Lintig J, Kiser PD, Golczak M, Palczewski K. The biochemical and structural basis for trans-to-cis isomerization of retinoids in the chemistry of vision. Trends in Biochemical Sciences. 2010 Jul;35(7):400–10. doi: 10.1016/j.tibs.2010.01.005.; Burns ME, Pugh EN. Lessons from photoreceptors: turning off g-protein signaling in living cells. Physiology (Bethesda). 2010 Apr;25(2):72–84. PMID: 20430952; PMCID: PMC2880230.; Blomhoff R, Blomhoff HK. Overview of retinoid metabolism and function. J Neurobiol. 2006 Jun;66(7):606–30. doi: 10.1002/neu.20242. PMID: 16688755.; Harrison EH. Mechanisms of digestion and absorption of dietary vitamin A. Annu Rev Nutr. 2005;25():87–103. doi: 10.1146/annurev.nutr.25.050304.092614. PMID: 16011460.; Wolf G. The visual cycle of the cone photoreceptors of the retina. Nutr Rev. 2004 Jul;62(7 Pt 1):283–6. doi: 10.1111/j.1753-4887.2004.tb00053.x. PMID: 15384919.; Harrison EH, Hussain MM. Mechanisms Involved in the Intestinal Digestion and Absorption of Dietary Vitamin A. The Journal of Nutrition. 2001 May;131(5):1405–8. doi: 10.1093/jn/131.5.1405.; Pugh EN, Lamb TD. Amplification and kinetics of the activation steps in phototransduction. Biochimica et Biophysica Acta (BBA) - Bioenergetics. 1993 Mar;1141(2-3):111–49. doi: 10.1016/0005-2728(93)90038-h.
RA biosynthesis pathway

Accession ID: Reactome:R-HSA-5365859
  • 10.1016/j.bbalip.2011.05.004
  • 10.1016/j.bmc.2013.11.025
 Das BC, Thapa P, Karki R, Das S, Mahapatra S, Liu T, Torregroza I, Wallace DP, Kambhampati S, Van Veldhuizen P, Verma A, Ray SK, Evans T. Retinoic acid signaling pathways in development and diseases. Bioorganic & Medicinal Chemistry. 2014 Jan;22(2):673–83. doi: 10.1016/j.bmc.2013.11.025.; Napoli JL. Physiological insights into all-trans-retinoic acid biosynthesis. Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids. 2012 Jan;1821(1):152–67. doi: 10.1016/j.bbalip.2011.05.004.
Diseases associated with visual transduction

Accession ID: Reactome:R-HSA-2474795
  • 10.1016/b978-0-12-384878-9.00006-6
  • 10.1016/j.preteyeres.2008.05.003
  • 10.1016/j.tips.2010.03.001
  • 10.1146/annurev.pharmtox.47.120505.105225
 Fletcher EL, Jobling AI, Vessey KA, Luu C, Guymer RH, Baird PN. Animal models of retinal disease. Prog Mol Biol Transl Sci. 2011;100():211–86. doi: 10.1016/b978-0-12-384878-9.00006-6. PMID: 21377628.; Palczewski K. Retinoids for treatment of retinal diseases. Trends in Pharmacological Sciences. 2010 Jun;31(6):284–95. doi: 10.1016/j.tips.2010.03.001.; den Hollander AI, Roepman R, Koenekoop RK, Cremers FPM. Leber congenital amaurosis: Genes, proteins and disease mechanisms. Progress in Retinal and Eye Research. 2008 Jul;27(4):391–419. doi: 10.1016/j.preteyeres.2008.05.003.; Travis GH, Golczak M, Moise AR, Palczewski K. Diseases Caused by Defects in the Visual Cycle: Retinoids as Potential Therapeutic Agents. Annu. Rev. Pharmacol. Toxicol. 2007 Feb 01;47(1):469–512. doi: 10.1146/annurev.pharmtox.47.120505.105225.
The retinoid cycle in cones (daylight vision)

Accession ID: Reactome:R-MMU-2187335
  • 10.1016/j.preteyeres.2010.11.001
  • 10.1074/jbc.r111.303008
  • 10.1074/jbc.r111.303990
  • 10.1111/j.1753-4887.2004.tb00053.x
 von Lintig J. Metabolism of Carotenoids and Retinoids Related to Vision. Journal of Biological Chemistry. 2012 Jan;287(3):1627–34. doi: 10.1074/jbc.r111.303990.; Kefalov VJ. Rod and Cone Visual Pigments and Phototransduction through Pharmacological, Genetic, and Physiological Approaches. Journal of Biological Chemistry. 2012 Jan;287(3):1635–41. doi: 10.1074/jbc.r111.303008.; Wang J, Kefalov VJ. The Cone-specific visual cycle. Progress in Retinal and Eye Research. 2011 Mar;30(2):115–28. doi: 10.1016/j.preteyeres.2010.11.001.; Wolf G. The visual cycle of the cone photoreceptors of the retina. Nutr Rev. 2004 Jul;62(7 Pt 1):283–6. doi: 10.1111/j.1753-4887.2004.tb00053.x. PMID: 15384919.
Signaling by Nuclear Receptors

Accession ID: Reactome:R-MMU-9006931
  • 10.1016/0039-128x(96)00030-x
  • 10.1016/bs.ctdb.2017.02.003
  • 10.1016/j.bbamcr.2009.11.012
  • 10.1016/j.bbamcr.2016.06.004
  • 10.1016/j.mce.2013.06.021
  • 10.1038/nrm.2016.122
  • 10.1210/me.2013-1334
 Holzer G, Markov GV, Laudet V. Evolution of Nuclear Receptors and Ligand Signaling: Toward a Soft Key-Lock Model? Curr Top Dev Biol. 2017;125():1–38. doi: 10.1016/bs.ctdb.2017.02.003. PMID: 28527568.; Levin ER, Hammes SR. Nuclear receptors outside the nucleus: extranuclear signalling by steroid receptors. Nature Reviews Molecular Cell Biology. 2016 Oct 12;17(12):783–97. doi: 10.1038/nrm.2016.122.; Schwartz N, Verma A, Bivens CB, Schwartz Z, Boyan BD. Rapid steroid hormone actions via membrane receptors. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research. 2016 Sep;1863(9):2289–98. doi: 10.1016/j.bbamcr.2016.06.004.; Simons SS, Edwards DP, Kumar R. Minireview: dynamic structures of nuclear hormone receptors: new promises and challenges. Mol Endocrinol. 2014 Feb;28(2):173–82. PMID: 24284822; PMCID: PMC3896641.; Hah N, Kraus WL. Hormone-regulated transcriptomes: Lessons learned from estrogen signaling pathways in breast cancer cells. Molecular and Cellular Endocrinology. 2014 Jan;382(1):652–64. doi: 10.1016/j.mce.2013.06.021.; Echeverria PC, Picard D. Molecular chaperones, essential partners of steroid hormone receptors for activity and mobility. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research. 2010 Jun;1803(6):641–9. doi: 10.1016/j.bbamcr.2009.11.012.; Beato M, Chávez S, Truss M. Transcriptional regulation by steroid hormones. Steroids. 1996 Apr;61(4):240–51. doi: 10.1016/0039-128x(96)00030-x. PMID: 8733009.
Visual phototransduction

Accession ID: Reactome:R-RNO-2187338
  • 10.1002/neu.20242
  • 10.1016/0005-2728(93)90038-h
  • 10.1016/j.preteyeres.2010.11.001
  • 10.1016/j.preteyeres.2012.05.002
  • 10.1016/j.tibs.2010.01.005
  • 10.1074/jbc.r111.303008
  • 10.1074/jbc.r111.303990
  • 10.1093/jn/131.5.1405
  • 10.1111/j.1753-4887.2004.tb00053.x
  • 10.1146/annurev.nutr.25.050304.092614
  • 10.1152/physiol.00001.2010
  • 10.3390/nu3010063
 Korenbrot JI. Speed, sensitivity, and stability of the light response in rod and cone photoreceptors: Facts and models. Progress in Retinal and Eye Research. 2012 Sep;31(5):442–66. doi: 10.1016/j.preteyeres.2012.05.002.; von Lintig J. Metabolism of Carotenoids and Retinoids Related to Vision. Journal of Biological Chemistry. 2012 Jan;287(3):1627–34. doi: 10.1074/jbc.r111.303990.; Kefalov VJ. Rod and Cone Visual Pigments and Phototransduction through Pharmacological, Genetic, and Physiological Approaches. Journal of Biological Chemistry. 2012 Jan;287(3):1635–41. doi: 10.1074/jbc.r111.303008.; Wang J, Kefalov VJ. The Cone-specific visual cycle. Progress in Retinal and Eye Research. 2011 Mar;30(2):115–28. doi: 10.1016/j.preteyeres.2010.11.001.; D'Ambrosio DN, Clugston RD, Blaner WS. Vitamin A metabolism: an update. Nutrients. 2011 Jan;3(1):63–103. PMID: 21350678; PMCID: PMC3042718.; von Lintig J, Kiser PD, Golczak M, Palczewski K. The biochemical and structural basis for trans-to-cis isomerization of retinoids in the chemistry of vision. Trends in Biochemical Sciences. 2010 Jul;35(7):400–10. doi: 10.1016/j.tibs.2010.01.005.; Burns ME, Pugh EN. Lessons from photoreceptors: turning off g-protein signaling in living cells. Physiology (Bethesda). 2010 Apr;25(2):72–84. PMID: 20430952; PMCID: PMC2880230.; Blomhoff R, Blomhoff HK. Overview of retinoid metabolism and function. J Neurobiol. 2006 Jun;66(7):606–30. doi: 10.1002/neu.20242. PMID: 16688755.; Harrison EH. Mechanisms of digestion and absorption of dietary vitamin A. Annu Rev Nutr. 2005;25():87–103. doi: 10.1146/annurev.nutr.25.050304.092614. PMID: 16011460.; Wolf G. The visual cycle of the cone photoreceptors of the retina. Nutr Rev. 2004 Jul;62(7 Pt 1):283–6. doi: 10.1111/j.1753-4887.2004.tb00053.x. PMID: 15384919.; Harrison EH, Hussain MM. Mechanisms Involved in the Intestinal Digestion and Absorption of Dietary Vitamin A. The Journal of Nutrition. 2001 May;131(5):1405–8. doi: 10.1093/jn/131.5.1405.; Pugh EN, Lamb TD. Amplification and kinetics of the activation steps in phototransduction. Biochimica et Biophysica Acta (BBA) - Bioenergetics. 1993 Mar;1141(2-3):111–49. doi: 10.1016/0005-2728(93)90038-h.
Signaling by Retinoic Acid

Accession ID: Reactome:R-RNO-5362517
  • 10.1016/j.bbalip.2011.05.004
  • 10.1016/j.bbalip.2011.06.002
  • 10.1016/j.bmc.2013.11.025
  • 10.1146/annurev-nutr-072610-145127
 Das BC, Thapa P, Karki R, Das S, Mahapatra S, Liu T, Torregroza I, Wallace DP, Kambhampati S, Van Veldhuizen P, Verma A, Ray SK, Evans T. Retinoic acid signaling pathways in development and diseases. Bioorganic & Medicinal Chemistry. 2014 Jan;22(2):673–83. doi: 10.1016/j.bmc.2013.11.025.; Harrison EH. Mechanisms involved in the intestinal absorption of dietary vitamin A and provitamin A carotenoids. Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids. 2012 Jan;1821(1):70–7. doi: 10.1016/j.bbalip.2011.06.002.; Napoli JL. Physiological insights into all-trans-retinoic acid biosynthesis. Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids. 2012 Jan;1821(1):152–67. doi: 10.1016/j.bbalip.2011.05.004.; Catharine Ross A, Zolfaghari R. Cytochrome P450s in the Regulation of Cellular Retinoic Acid Metabolism. Annu. Rev. Nutr. 2011 Aug 21;31(1):65–87. doi: 10.1146/annurev-nutr-072610-145127.
Signaling Pathways

Accession ID: Reactome:R-SPO-162582
  • 10.1016/j.bbcan.2006.09.001
  • 10.1016/j.cell.2007.06.009
  • 10.1016/j.cell.2009.03.045
  • 10.1016/j.cytogfr.2004.04.003
  • 10.1016/j.cytogfr.2005.01.001
  • 10.1016/j.devcel.2009.06.016
  • 10.1016/j.tcb.2009.05.008
  • 10.1016/j.tibs.2005.10.005
  • 10.1038/414799a
  • 10.1038/nature08144
  • 10.1038/nrm1498
  • 10.1038/nrm2299
  • 10.1038/nrm2717
  • 10.1038/nrm2803
  • 10.1038/nrm3048
  • 10.1038/sj.onc.1210394
  • 10.1093/jb/mvp148
  • 10.1098/rstb.2006.1894
  • 10.1101/gad.1653708
  • 10.3109/09687688.2011.603101
 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 Nuclear Receptors

Accession ID: Reactome:R-SPO-9006931
  • 10.1016/0039-128x(96)00030-x
  • 10.1016/bs.ctdb.2017.02.003
  • 10.1016/j.bbamcr.2009.11.012
  • 10.1016/j.bbamcr.2016.06.004
  • 10.1016/j.mce.2013.06.021
  • 10.1038/nrm.2016.122
  • 10.1210/me.2013-1334
 Holzer G, Markov GV, Laudet V. Evolution of Nuclear Receptors and Ligand Signaling: Toward a Soft Key-Lock Model? Curr Top Dev Biol. 2017;125():1–38. doi: 10.1016/bs.ctdb.2017.02.003. PMID: 28527568.; Levin ER, Hammes SR. Nuclear receptors outside the nucleus: extranuclear signalling by steroid receptors. Nature Reviews Molecular Cell Biology. 2016 Oct 12;17(12):783–97. doi: 10.1038/nrm.2016.122.; Schwartz N, Verma A, Bivens CB, Schwartz Z, Boyan BD. Rapid steroid hormone actions via membrane receptors. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research. 2016 Sep;1863(9):2289–98. doi: 10.1016/j.bbamcr.2016.06.004.; Simons SS, Edwards DP, Kumar R. Minireview: dynamic structures of nuclear hormone receptors: new promises and challenges. Mol Endocrinol. 2014 Feb;28(2):173–82. PMID: 24284822; PMCID: PMC3896641.; Hah N, Kraus WL. Hormone-regulated transcriptomes: Lessons learned from estrogen signaling pathways in breast cancer cells. Molecular and Cellular Endocrinology. 2014 Jan;382(1):652–64. doi: 10.1016/j.mce.2013.06.021.; Echeverria PC, Picard D. Molecular chaperones, essential partners of steroid hormone receptors for activity and mobility. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research. 2010 Jun;1803(6):641–9. doi: 10.1016/j.bbamcr.2009.11.012.; Beato M, Chávez S, Truss M. Transcriptional regulation by steroid hormones. Steroids. 1996 Apr;61(4):240–51. doi: 10.1016/0039-128x(96)00030-x. PMID: 8733009.