Abstract
Alzheimer’s disease (AD) is a complex neurodegenerative disorder in which loss of neurons and synaptic function causes dementia in the elderly. To clarify AD pathogenesis and develop drugs for AD, thousands of studies have elucidated signaling pathways involved. However, knowledge of AD signaling pathways has not been compiled as a pathway map. In this chapter, we introduce the manual construction of a pathway map in AD which we call “AlzPathway”, that comprehensively catalogs signaling pathways in the field of AD. We have collected and manually curated over 100 review articles related to AD, and have built the AD pathway map. AlzPathway is currently composed of thousands of molecules and reactions in neurons, brain blood barrier, presynaptic, postsynaptic, astrocyte, and microglial cells, with their cellular localizations. AlzPathway provides a systems-biology platform of comprehensive AD signaling and related pathways which is expected to contribute to clarification of AD pathogenesis and AD drug development.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Alzheimer’s Society (2013) What is Alzheimer’s disease? Alzheimers.org.uk. Last updated Mar 2012
Bertram L, McQueen MB, Mullin K et al (2007) Systematic meta-analyses of Alzheimer disease genetic association studies: the AlzGene database. Nat Genet 39:17–23
Mizuno S, Iijima R, Ogishima S et al (2012) AlzPathway: a comprehensive map of signaling pathways of Alzheimer’s disease. BMC Syst Biol 6:52
Funahashi A, Matsuoka Y, Jouraku A et al (2008) Cell Designer 3.5: a versatile modeling tool for biochemical networks. Proc IEEE 96:1254–1265
Laibe C, Le Novère N (2007) MIRIAM resources: tools to generate and resolve robust cross-references in systems biology. BMC Syst Biol 1:58
Guerreiro R, Wojtas A, Bras J et al (2013) TREM2 variants in Alzheimer’s disease. N Engl J Med 368:117–127
Jonsson T, Stefansson H, Steinberg S et al (2013) Variant of TREM2 associated with the risk of Alzheimer’s disease. N Engl J Med 368:107–116
Hucka M, Finney A, Sauro HM et al (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19:524–531
Matsuoka Y, Ghosh S, Kikuchi N, Kitano H (2010) Payao: a community platform for SBML pathway model curation. Bioinformatics 26:1381–1383
Oda K, Matsuoka Y, Funahashi A, Kitano H (2005) A comprehensive pathway map of epidermal growth factor receptor signaling. Mol Syst Biol 1:2005.0010
Oda K, Kitano H (2006) A comprehensive map of the toll-like receptor signaling network. Mol Syst Biol 2:2006.0015
Calzone L, Gelay A, Zinovyev A et al (2008) A comprehensive modular map of molecular interactions in RB/E2F pathway. Mol Syst Biol 4:173
Caron E, Ghosh S, Matsuoka Y et al (2010) A comprehensive map of the mTOR signaling network. Mol Syst Biol 6:453
Le Novère N, Hucka M, Mi H et al (2009) The systems biology graphical notation. Nat Biotechnol 27:735–741
Smoot ME, Ono K, Ruscheinski J et al (2011) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27:431–432
Girvan M, Newman ME (2002) Community structure in social and biological networks. Proc Natl Acad Sci U S A 99:7821–7826
Fujita KA, Ostaszewski M, Matsuoka Y et al (2013) Integrating pathways of Parkinson’s disease in a molecular interaction map. Mol Neurobiol 49:88–102
Acknowledgements
This work was supported by a Grant-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science, and Technology of Japan.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2016 Springer Science+Business Media New York
About this protocol
Cite this protocol
Ogishima, S. et al. (2016). AlzPathway, an Updated Map of Curated Signaling Pathways: Towards Deciphering Alzheimer’s Disease Pathogenesis. In: Castrillo, J., Oliver, S. (eds) Systems Biology of Alzheimer's Disease. Methods in Molecular Biology, vol 1303. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2627-5_25
Download citation
DOI: https://doi.org/10.1007/978-1-4939-2627-5_25
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-2626-8
Online ISBN: 978-1-4939-2627-5
eBook Packages: Springer Protocols