AutismKB: An evidence-based knowledgebase of autism genetics

Nucleic Acids Research

Volumn 40, Issue D1, 2012, Pages

  Xu, Li Ming ^a   Li, Jia Rui ^a   Huang, Yue ^a   Zhao, Min ^a   Tang, Xing ^a   Wei, Liping ^a  

^a PEKING UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTISM; AUTISMKB DATA BASE; COPY NUMBER VARIATION; DEMOGRAPHY; GENE EXPRESSION PROFILING; GENE MAPPING; GENETIC ASSOCIATION; GENETIC LINKAGE; HUMAN; KNOWLEDGE BASE; PREVALENCE; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; SCORING SYSTEM; SINGLE NUCLEOTIDE POLYMORPHISM; VARIABLE NUMBER OF TANDEM REPEAT;

AUTISTIC DISORDER; DATABASES, GENETIC; GENETIC LINKAGE; GENETIC VARIATION; HUMANS; KNOWLEDGE BASES; MOLECULAR SEQUENCE ANNOTATION; USER-COMPUTER INTERFACE;

EID: 84862224852     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr1145     Document Type: Article

References (62)

1. American Psychiatric Association. (2000) Diagnostic and Statistical Manual of Mental Disorders: DSM-IV-TR. American Psychiatric Publishing, Inc, Arlington, VA.
2. Kogan,M.D., Blumberg,S.J., Schieve,L.A., Boyle,C.A., Perrin,J.M., Ghandour,R.M., Singh,G.K., Strickland,B.B., Trevathan,E. and van Dyck,P.C. (2009) prevalence of parent-reported diagnosis of autism spectrum disorder among children in the US, 2007. Pediatrics, 124, 1395-1403.
3. Kim,Y.S., Leventhal,B.L., Koh,Y.J., Fombonne,E., Laska,E., Lim,E.C., Cheon,K.A., Kim,S.J., Kim,Y.K., Lee,H. et al. (2011) Prevalence of autism spectrum disorders in a total population sample. Am. J. Psychiatry, 168, 904-912.
4. Ganz,M.L. (2006) The Costs of Autism. In: Moldin,S.O. and Rubenstein,J.L.R. (eds), Understanding Autism: from Basic Neuroscience to Treatment. CRC Press, Boca Raton, FL, pp. 476-498.
5. Hallmayer,J., Cleveland,S., Torres,A., Phillips,J., Cohen,B., Torigoe,T., Miller,J., Fedele,A., Collins,J., Smith,K. et al. (2011) Genetic heritability and shared environmental factors among twin pairs with autism. Arch. Gen. Psychiatry, 68, 1095-1102.
6. Bailey,A., Le Couteur,A., Gottesman,I., Bolton,P., Simonoff,E., Yuzda,E. and Rutter,M. (1995) Autism as a strongly genetic disorder: evidence from a British twin study. Psychol. Med., 25, 63-77.
7. Betancur,C. (2011) Etiological heterogeneity in autism spectrum disorders: more than 100 genetic and genomic disorders and still counting. Brain Res., 1380, 42-77.
8. Abrahams,B.S. and Geschwind,D.H. (2008) Advances in autism genetics: on the threshold of a new neurobiology. Nat. Rev. Genet., 9, 341-355. (Pubitemid 351556064)
9. State,M.W. (2010) The genetics of child psychiatric disorders: focus on autism and Tourette syndrome. Neuron, 68, 254-269.
10. Lander,E.S. (2011) Initial impact of the sequencing of the human genome. Nature, 470, 187-197.
11. Banerjee-Basu,S. and Packer,A. (2010) SFARI Gene: an evolving database for the autism research community. Dis. Model Mech., 3, 133-135.
12. Basu,S.N., Kollu,R. and Banerjee-Basu,S. (2009) AutDB: a gene reference resource for autism research. Nucleic Acids Res., 37, D832-D836.
13. Matuszek,G. and Talebizadeh,Z. (2009) Autism Genetic Database (AGD): a comprehensive database including autism susceptibility gene-CNVs integrated with known noncoding RNAs and fragile sites. BMC Med. Genet., 10, 102.
14. Marshall,C.R., Noor,A., Vincent,J.B., Lionel,A.C., Feuk,L., Skaug,J., Shago,M., Moessner,R., Pinto,D., Ren,Y. et al. (2008) Structural variation of chromosomes in autism spectrum disorder. Am. J. Hum. Genet., 82, 477-488.
15. Fujita,P.A., Rhead,B., Zweig,A.S., Hinrichs,A.S., Karolchik,D., Cline,M.S., Goldman,M., Barber,G.P., Clawson,H., Coelho,A. et al. (2011) The UCSC Genome Browser database: update 2011. Nucleic Acids Res., 39, D876-D882.
16. Sun,J., Jia,P., Fanous,A.H., Webb,B.T., van den Oord,E.J., Chen,X., Bukszar,J., Kendler,K.S. and Zhao,Z. (2009) A multi-dimensional evidence-based candidate gene prioritization approach for complex diseases-schizophrenia as a case. Bioinformatics, 25, 2595-6602.
17. Freitag,C.M. (2007) The genetics of autistic disorders and its clinical relevance: a review of the literature. Mol. Psychiatry, 12, 2-22.
18. Klauck,S.M. (2006) Genetics of autism spectrum disorder. Eur. J. Hum. Genet., 14, 714-720.
19. Losh,M., Sullivan,P.F., Trembath,D. and Piven,J. (2008) Current developments in the genetics of autism: from phenome to genome. J. Neuropathol. Exp. Neurol., 67, 829-837.
20. Muhle,R., Trentacoste,S.V. and Rapin,I. (2004) The genetics of autism. Pediatrics, 113, e472-e486.
21. Sayers,E.W., Barrett,T., Benson,D.A., Bolton,E., Bryant,S.H., Canese,K., Chetvernin,V., Church,D.M., DiCuccio,M., Federhen,S. et al. (2011) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 39, D38-51.
22. Stark,C., Breitkreutz,B.J., Chatr-Aryamontri,A., Boucher,L., Oughtred,R., Livstone,M.S., Nixon,J., Van Auken,K., Wang,X., Shi,X. et al. (2011) The BioGRID Interaction Database: 2011 update. Nucleic Acids Res., 39, D698-704.
23. Gilbert,D. (2005) Biomolecular interaction network database. Brief Bioinform., 6, 194-198.
24. Keshava Prasad,T.S., Goel,R., Kandasamy,K., Keerthikumar,S., Kumar,S., Mathivanan,S., Telikicherla,D., Raju,R., Shafreen,B., Venugopal,A. et al. (2009) Human Protein Reference Database - 2009 update. Nucleic Acids Res., 37, D767-D772.
25. Zhang,J., Feuk,L., Duggan,G.E., Khaja,R. and Scherer,S.W. (2006) Development of bioinformatics resources for display and analysis of copy number and other structural variants in the human genome. Cytogenet Genome Res., 115, 205-214. (Pubitemid 44832022)
26. Bertram,L., McQueen,M.B., Mullin,K., Blacker,D. and Tanzi,R.E. (2007) Systematic meta-analyses of Alzheimer disease genetic association studies: the AlzGene database. Nat. Genet., 39, 17-23. (Pubitemid 46026496)
27. Allen,N.C., Bagade,S., McQueen,M.B., Ioannidis,J.P., Kavvoura,F.K., Khoury,M.J., Tanzi,R.E. and Bertram,L. (2008) Systematic meta-analyses and field synopsis of genetic association studies in schizophrenia: the SzGene database. Nat. Genet., 40, 827-834. (Pubitemid 351913655)
28. Blake,J.A., Bult,C.J., Kadin,J.A., Richardson,J.E. and Eppig,J.T. (2011) The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics. Nucleic Acids Res., 39, D842-D848.
29. Bradford,Y., Conlin,T., Dunn,N., Fashena,D., Frazer,K., Howe,D.G., Knight,J., Mani,P., Martin,R., Moxon,S.A. et al. (2011) ZFIN: enhancements and updates to the Zebrafish Model Organism Database. Nucleic Acids Res., 39, D822-D829.
30. Tweedie,S., Ashburner,M., Falls,K., Leyland,P., McQuilton,P., Marygold,S., Millburn,G., Osumi-Sutherland,D., Schroeder,A., Seal,R. et al. (2009) FlyBase: enhancing Drosophila Gene Ontology annotations. Nucleic Acids Res., 37, D555-D559.
31. Su,A.I., Wiltshire,T., Batalov,S., Lapp,H., Ching,K.A., Block,D., Zhang,J., Soden,R., Hayakawa,M., Kreiman,G. et al. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl Acad. Sci. USA, 101, 6062-6067. (Pubitemid 38520528)
32. Jones,A.R., Overly,C.C. and Sunkin,S.M. (2009) The Allen Brain Atlas: 5 years and beyond. Nat. Rev. Neurosci., 10, 821-828.
33. Wang,E.T., Sandberg,R., Luo,S., Khrebtukova,I., Zhang,L., Mayr,C., Kingsmore,S.F., Schroth,G.P. and Burge,C.B. (2008) Alternative isoform regulation in human tissue transcriptomes. Nature, 456, 470-476. (Pubitemid 352759009)
34. Wu,J.Q., Habegger,L., Noisa,P., Szekely,A., Qiu,C., Hutchison,S., Raha,D., Egholm,M., Lin,H., Weissman,S. et al. (2010) Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing. Proc. Natl Acad. Sci. USA, 107, 5254-5259.
35. Langmead,B., Trapnell,C., Pop,M. and Salzberg,S.L. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
36. Mortazavi,A., Williams,B.A., McCue,K., Schaeffer,L. and Wold,B. (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods, 5, 621-628. (Pubitemid 351911867)
37. Trapnell,C., Pachter,L. and Salzberg,S.L. (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25, 1105-1111.
38. Trapnell,C., Williams,B.A., Pertea,G., Mortazavi,A., Kwan,G., van Baren,M.J., Salzberg,S.L., Wold,B.J. and Pachter,L. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol., 28, 511-515.
39. Vizcaino,J.A., Cote,R., Reisinger,F., Foster,J.M., Mueller,M., Rameseder,J., Hermjakob,H. and Martens,L. (2009) A guide to the Proteomics Identifications Database proteomics data repository. Proteomics, 9, 4276-4283.
40. Farrah,T., Deutsch,E.W., Omenn,G.S., Campbell,D.S., Sun,Z., Bletz,J.A., Mallick,P., Katz,J.E., Malmstrom,J., Ossola,R. et al. (2011) A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. Mol. Cell Proteomics, 10, M110 006353.
41. Dweep,H., Sticht,C., Pandey,P. and Gretz,N. (2011) miRWalk - Database: Prediction of possible miRNA binding sites by 'walking' the genes of three genomes. J. Biomed Inform, 44, 839-847.
42. Papadopoulos,G.L., Reczko,M., Simossis,V.A., Sethupathy,P. and Hatzigeorgiou,A.G. (2009) The database of experimentally supported targets: a functional update of TarBase. Nucleic Acids Res., 37, D155-D158.
43. Zhang,Y., Liu,X.S., Liu,Q.R. and Wei,L. (2006) Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species. Nucleic Acids Res., 34, 3465-3475.
44. Lee,T.Y., Hsu,J.B., Chang,W.C., Wang,T.Y., Hsu,P.C. and Huang,H.D. (2009) A comprehensive resource for integrating and displaying protein post-translational modifications. BMC Res. Notes, 2, 111.
45. Xie,C., Mao,X., Huang,J., Ding,Y., Wu,J., Dong,S., Kong,L., Gao,G., Li,C.Y. and Wei,L. (2011) KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res., 39, W316-W322.
46. Karp,P.D., Ouzounis,C.A., Moore-Kochlacs,C., Goldovsky,L., Kaipa,P., Ahren,D., Tsoka,S., Darzentas,N., Kunin,V. and Lopez-Bigas,N. (2005) Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res., 33, 6083-6089. (Pubitemid 41742547)
47. Kanehisa,M., Araki,M., Goto,S., Hattori,M., Hirakawa,M., Itoh,M., Katayama,T., Kawashima,S., Okuda,S., Tokimatsu,T. et al. (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res., 36, D480-D484. (Pubitemid 351149770)
48. Schaefer,C.F., Anthony,K., Krupa,S., Buchoff,J., Day,M., Hannay,T. and Buetow,K.H. (2009) PID: the Pathway Interaction Database. Nucleic Acids Res., 37, D674-D679.
49. Thomas,P.D., Campbell,M.J., Kejariwal,A., Mi,H., Karlak,B., Daverman,R., Diemer,K., Muruganujan,A. and Narechania,A. (2003) PANTHER: a library of protein families and subfamilies indexed by function. Genome Res., 13, 2129-2141. (Pubitemid 37161770)
50. Croft,D., O'Kelly,G., Wu,G., Haw,R., Gillespie,M., Matthews,L., Caudy,M., Garapati,P., Gopinath,G., Jassal,B. et al. (2011) Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res., 39, D691-D697.
51. Kanehisa,M., Goto,S., Furumichi,M., Tanabe,M. and Hirakawa,M. (2010) KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res., 38, D355-D360.
52. Osborne,J.D., Flatow,J., Holko,M., Lin,S.M., Kibbe,W.A., Zhu,L.J., Danila,M.I., Feng,G. and Chisholm,R.L. (2009) Annotating the human genome with Disease Ontology. BMC Genomics, 10(Suppl. 1), S6.
53. Du,P., Feng,G., Flatow,J., Song,J., Holko,M., Kibbe,W.A. and Lin,S.M. (2009) From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations. Bioinformatics, 25, i63-i68.
54. Becker,K.G., Barnes,K.C., Bright,T.J. and Wang,S.A. (2004) The genetic association database. Nat. Genet., 36, 431-432.
55. Hindorff,L.A., Sethupathy,P., Junkins,H.A., Ramos,E.M., Mehta,J.P., Collins,F.S. and Manolio,T.A. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl Acad. Sci USA, 106, 9362-9367.
56. Davis,A.P., King,B.L., Mockus,S., Murphy,C.G., Saraceni-Richards,C., Rosenstein,M., Wiegers,T. and Mattingly,C.J. (2011) The Comparative Toxicogenomics Database: update 2011. Nucleic Acids Res., 39, D1067-D1072.
57. Relling,M.V., Gardner,E.E., Sandborn,W.J., Schmiegelow,K., Pui,C.H., Yee,S.W., Stein,C.M., Carrillo,M., Evans,W.E. and Klein,T.E. (2011) Clinical Pharmacogenetics Implementation Consortium guidelines for thiopurine methyltransferase genotype and thiopurine dosing. Clin. Pharmacol. Ther., 89, 387-391.
58. Knox,C., Law,V., Jewison,T., Liu,P., Ly,S., Frolkis,A., Pon,A., Banco,K., Mak,C., Neveu,V. et al. (2011) DrugBank 3.0: a comprehensive resource for 'omics' research on drugs. Nucleic Acids Res., 39, D1035-D1041.
59. Huang da,W., Sherman,B.T. and Lempicki,R.A. (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc., 4, 44-57.
60. Gilman,S.R., Iossifov,I., Levy,D., Ronemus,M., Wigler,M. and Vitkup,D. (2011) Rare de novo variants associated with autism implicate a large functional network of genes involved in formation and function of synapses. Neuron, 70, 898-907.
61. Voineagu,I., Wang,X., Johnston,P., Lowe,J.K., Tian,Y., Horvath,S., Mill,J., Cantor,R.M., Blencowe,B.J. and Geschwind,D.H. (2011) Transcriptomic analysis of autistic brain reveals convergent molecular pathology. Nature, 474, 380-384.
62. Liu,X., Wu,J., Wang,J., Zhao,S., Li,Z., Kong,L., Gu,X., Luo,J. and Gao,G. (2009) WebLab: a data-centric, knowledge-sharing bioinformatic platform. Nucleic Acids Res., 37, W33-W39.