REFERENCES 1. Husi,H., Ward,M.A., Choudhary,J.S., Blackstock,W.P. and Grant,S.G. (2000) Proteomic analysis of NMDA receptor-adhesion protein signaling complexes. Nat. Neurosci., 3, 661–669. 2. Collins,M.O., Husi,H., Yu,L., Brandon,J.M., Anderson,C.N., Blackstock,W.P., Choudhary,J.S. and Grant,S.G. (2006) Molecular characterization and comparison of the components and multipro- tein complexes in the postsynaptic proteome. J. Neurochem., 97 (Suppl 1), 16–23. 3. Takamori,S., Holt,M., Stenius,K., Lemke,E.A., Gronborg,M., Riedel,D., Urlaub,H., Schenck,S., Brugger,B., Ringler,P. et al. (2006) Molecular anatomy of a traﬃcking organelle. Cell, 127, 831–846. 4. Zhang,W., Zhang,Y., Zheng,H., Zhang,C., Xiong,W., Olyarchuk,J.G., Walker,M., Xu,W., Zhao,M., Zhao,S. et al. (2007) SynDB: a Synapse protein DataBase based on synapse ontology. Nucleic Acids Res., 35, D737–D741. 5. Grant,S.G., Marshall,M.C., Page,K.L., Cumiskey,M.A. and Armstrong,J.D. (2005) Synapse proteomics of multiprotein com- plexes: en route from genes to nervous system diseases. Hum. Mol. Genet., 14 (Spec No. 2), R225–R234. 6. Grant,S.G. (2006) The synapse proteome and phosphoproteome: a new paradigm for synapse biology. Biochem. Soc. Trans., 34, 59–63. 7. Emes,R.D., Pocklington,A.J., Anderson,C.N., Bayes,A., Collins,M.O., Vickers,C.A., Croning,M.D., Malik,B.R., Choudhary,J.S., Armstrong,J.D. et al. (2008) Evolutionary expansion and anatomical specialization of synapse proteome complexity. Nat. Neurosci., 11, 799–806. 8. Pearson,W.R. (1990) Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol., 183, 63–98. 9. Bult,C.J., Eppig,J.T., Kadin,J.A., Richardson,J.E., Blake,J.A. and Mouse Genome Database Group, (2008) The Mouse Genome Database (MGD): mouse biology and model systems. Nucleic Acids Res., 36, D724–D728. 10. Bruford,E.A., Lush,M.J., Wright,M.W., Sneddon,T.P., Povey,S. and Birney,E. (2008) The HGNC Database in 2008: a resource for the human genome. Nucleic Acids Res., 36, D445–D448. 11. The UniProt Consortium (2008) The universal protein resource (UniProt). Nucleic Acids Res., 36, D190–D195. 12. Sheng,M. and Hoogenraad,C.C. (2007) The postsynaptic architecture of excitatory synapses: a more quantitative view. Annu. Rev. Biochem., 76, 823–847. 13. Mills,I.G. (2007) The interplay between clathrin-coated vesicles and cell signalling. Semin. Cell Dev. Biol., 18, 459–470. 14. Pocklington,A.J., Cumiskey,M., Armstrong,J.D. and Grant,S.G. (2006) The proteomes of neurotransmitter receptor complexes form modular networks with distributed functionality underlying plasticity and behaviour. Mol. Syst. Biol., 2, 2006.0023. 15. Flicek,P., Aken,B.L., Beal,K., Ballester,B., Caccamo,M., Chen,Y., Clarke,L., Coates,G., Cunningham,F., Cutts,T. et al. (2008) Ensembl 2008. Nucleic Acids Res., 36, D707–D714. 16. Wilming,L.G., Gilbert,J.G., Howe,K., Trevanion,S., Hubbard,T. and Harrow,J.L. (2008) The vertebrate genome annotation (Vega) database. Nucleic Acids Res., 36, D753–D760. 17. Maglott,D., Ostell,J., Pruitt,K.D. and Tatusova,T. (2007) Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res., 35, D26–D31. 18. Safran,M., Chalifa-Caspi,V., Shmueli,O., Olender,T., Lapidot,M., Rosen,N., Shmoish,M., Peter,Y., Glusman,G., Feldmesser,E. et al. (2003) Human Gene-Centric Databases at the Weizmann Institute of Science: GeneCards, UDB, CroW 21 and HORDE. Nucleic Acids Res., 31, 142–146. Nucleic Acids Research, 2009, Vol. 37, Database issue D851 19. McKusick,V.A. (2007) Mendelian inheritance in man and its online version, OMIM. Am. J. Hum. Genet., 80, 588–604. 20. Toouli,J. (2008) PubMed Central. HPB, 10, 3. 21. Lein,E.S., Hawrylycz,M.J., Ao,N., Ayres,M., Bensinger,A., Bernard,A., Boe,A.F., Boguski,M.S., Brockway,K.S., Byrnes,E.J. et al. (2007) Genome-wide atlas of gene expression in the adult mouse brain. Nature, 445, 168–176. 22. Magdaleno,S., Jensen,P., Brumwell,C.L., Seal,A., Lehman,K., Asbury,A., Cheung,T., Cornelius,T., Batten,D.M., Eden,C. et al. (2006) BGEM: an in situ hybridization database of gene expression in the embryonic and adult mouse nervous system. PLoS Biol., 4, e86. 23. Visel,A., Thaller,C. and Eichele,G. (2004) GenePaint.org: an atlas of gene expression patterns in the mouse embryo. Nucleic Acids Res., 32, D552–D556. 24. Heintz,N. (2004) Gene expression nervous system atlas (GENSAT). Nat. Neurosci., 7, 483. 25. Venkataraman,S., Stevenson,P., Yang,Y., Richardson,L., Burton,N., Perry,T.P., Smith,P., Baldock,R.A., Davidson,D.R. and Christiansen,J.H. (2008) EMAGE—Edinburgh Mouse Atlas of Gene Expression: 2008 update. Nucleic Acids Res., 36, D860–D865. 26. Berglund,L., Bjorling,E., Oksvold,P., Fagerberg,L., Asplund,A., Al-Khalili Szigyarto,C., Persson,A., Ottosson,J., Wernerus,H., Nilsson,P. et al. (2008) A gene-centric human protein atlas for expression proﬁles based on antibodies. Mol. Cell Proteomics, 7, 2019–2027. 27. Armstrong,J.D., Pocklington,A.J., Cumiskey,M.A. and Grant,S.G. (2006) Reconstructing protein complexes: from proteomics to systems biology. Proteomics, 6, 4724–4731. 28. Hatcher,E. and Gospodnetic,O. (2004) Lucene In Action, Manning Publishers, Greenwich. 29. Grant,S.G.N. (2003) An integrative neuroscience programme linking mouse genes to cognition and disease. In Plomin,R., Defries,J.C., Craig,I.W. and McGuﬃn,P. (eds), Behavioural Genetics in the Post Genomic Era, APA Books, Washington, DC, pp. 123–138. 30. Jordan,B.A., Fernholz,B.D., Boussac,M., Xu,C., Grigorean,G., Ziﬀ,E.B. and Neubert,T.A. (2004) Identiﬁcation and veriﬁcation of novel rodent postsynaptic density proteins. Mol. Cell Proteomics, 3, 857–871. 31. Li,K.W., Hornshaw,M.P., Van Der Schors,R.C., Watson,R., Tate,S., Casetta,B., Jimenez,C.R., Gouwenberg,Y., Gundelﬁnger,E.D., Smalla,K.H. et al. (2004) Proteomics analysis of rat brain postsynaptic density. Implications of the diverse protein functional groups for the integration of synaptic physiology. J. Biol. Chem., 279, 987–1002. 32. Peng,J., Kim,M.J., Cheng,D., Duong,D.M., Gygi,S.P. and Sheng,M. (2004) Semiquantitative proteomic analysis of rat fore- brain postsynaptic density fractions by mass spectrometry. J. Biol. Chem., 279, 21003–21011. 33. Yoshimura,Y., Yamauchi,Y., Shinkawa,T., Taoka,M., Donai,H., Takahashi,N., Isobe,T. and Yamauchi,T. (2004) Molecular constituents of the postsynaptic density fraction revealed by proteomic analysis using multidimensional liquid chromatography-tandem mass spectrometry. J. Neurochem., 88, 759–768. 34. Satoh,K., Takeuchi,M., Oda,Y., Deguchi-Tawarada,M., Sakamoto,Y., Matsubara,K., Nagasu,T. and Takai,Y. (2002) Identiﬁcation of activity-regulated proteins in the postsynaptic density fraction. Genes Cells, 7, 187–197. 35. Walikonis,R.S., Jensen,O.N., Mann,M., Provance,D.W. Jr., Mercer,J.A. and Kennedy,M.B. (2000) Identiﬁcation of proteins in the postsynaptic density fraction by mass spectrometry. J. Neurosci., 20, 4069–4080.