SynaptomeDB: An ontology-based knowledgebase for synaptic genes

Bioinformatics

Volumn 28, Issue 6, 2012, Pages 897-899

  Pirooznia, Mehdi ^a   Wang, Tao ^b   Avramopoulos, Dimitrios ^b   Valle, David ^b   Thomas, Gareth ^a   Huganir, Richard L ^a   Goes, Fernando S ^a   Potash, James B ^c   Zandi, Peter P ^a,d  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b JOHNS HOPKINS UNIVERSITY   (United States)

^c UNIVERSITY OF IOWA   (United States)

^d JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ARTICLE; GENETIC DATABASE; GENETICS; GENOMICS; HUMAN; INTERNET; KNOWLEDGE BASE; METABOLISM; SYNAPSE;

DATABASES, GENETIC; GENOMICS; HUMANS; INTERNET; KNOWLEDGE BASES; PROTEINS; SYNAPSES;

EID: 84859032917     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts040     Document Type: Article

References (24)

1. Abul-Husn, N. S. et al. (2009) Systems approach to explore components and interactions in the presynapse. Proteomics, 9, 3303-3315.
2. Allen, N. C. et al. (2008) Systematic meta-analyses and field synopsis of genetic association studies in schizophrenia: the SzGene database. Nat. Genet., 40, 827-834.
3. Ashburner, M. et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
4. Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc., 57, 289-300.
5. Berman, H. M. et al. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
6. Bertram, L. et al. (2007) Systematic meta-analyses of Alzheimer disease genetic association studies: the AlzGene database. Nat. Genet., 39, 17-23.
7. Chua, J. J. et al. (2010) The architecture of an excitatory synapse. J. Cell Sci., 123, 819-823.
8. Ferreira, M. A. et al. (2008) Collaborative genome-wide association analysis supports a role for ANK3 and CACNA1C in bipolar disorder. Nat. Genet., 40, 1056-1058.
9. Flicek, P. et al. (2011) Ensembl 2011. Nucleic Acids Res., 39, D800-D806.
10. Fury, W. et al. (2006) Overlapping probabilities of top ranking gene lists, hypergeometric distribution, and stringency. Conf. Proc. IEEE Eng. Med. Biol. Soc., 1, 5531-5534.
11. Gauthier, J. et al. (2009) Novel de novo SHANK3 mutation in autistic patients. Am. J. Med. Genet. B Neuropsychiatr. Genet., 150B, 421-424.
12. Glessner, J. T. et al. (2010) Strong synaptic transmission impact by copy number variations in schizophrenia. Proc. Natl Acad. Sci. USA, 107, 10584-10589.
13. Goujon, M. et al. (2010) A new bioinformatics analysis tools framework at EMBL-EBI. Nucleic Acids Res., 38, W695-W699.
14. Holmans, P. (2010) Statistical methods for pathway analysis of genome-wide data for association with complex genetic traits. Adv. Genet., 72, 141-179.
15. Kahler, A. K. et al. (2010) Association study of PDE4B gene variants in Scandinavian schizophrenia and bipolar disorder multicenter case-control samples. Am. J. Med. Genet. B Neuropsychiatr. Genet., 153B, 86-96.
16. Keshava Prasad, T. S. et al. (2009) Human Protein Reference Database-2009 update. Nucleic Acids Res., 37, D767-D772.
17. Kirov, S. A. et al. (2005) GeneKeyDB: a lightweight, gene-centric, relational database to support data mining environments. BMC Bioinformatics, 6, 72.
18. Liberzon, A. et al. (2011) Molecular signatures database (MSigDB) 3. 0. Bioinformatics, 27, 1739-1740.
19. Mudunuri, U. et al. (2009) bioDBnet: the biological database network. Bioinformatics, 25, 555-556.
20. Shyn, S. I. et al. (2011) Novel loci for major depression identified by genome-wide association study of sequenced treatment alternatives to relieve depression and meta-analysis of three studies. Mol. Psychiatry, 16, 202-215.
21. Stajich, J. E. et al. (2002) The Bioperl toolkit: Perl modules for the life sciences. Genome Res., 12, 1611-1618.
22. von Mering, C. et al. (2003) STRING: a database of predicted functional associations between proteins. Nucleic Acids Res., 31, 258-261.
23. Wu, H. et al. (2010) To build a synapse: signaling pathways in neuromuscular junction assembly. Development, 137, 1017-1033.
24. Zhang, W. et al. (2007) SynDB: a Synapse protein DataBase based on synapse ontology. Nucleic Acids Res., 35, D737-D741.