T1DBase: Update 2011, organization and presentation of large-scale data sets for type 1 diabetes research

Nucleic Acids Research

Volumn 39, Issue SUPPL. 1, 2011, Pages

  Burren, Oliver S ^a   Adlem, Ellen C ^a   Achuthan, Premanand ^a   Christensen, Mikkel ^a   Coulson, Richard M R ^a   Todd, John A ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER PROGRAM; CYTOGENETICS; DATA BASE; GENE EXPRESSION; GENE LOCUS; GENETIC ASSOCIATION; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; GENOTYPE; HUMAN; INFORMATION PROCESSING; INSULIN DEPENDENT DIABETES MELLITUS; INTERNET; MEDICAL RESEARCH; NONHUMAN; PRIORITY JOURNAL; SEARCH ENGINE; SINGLE NUCLEOTIDE POLYMORPHISM; T1DBASE DATABASE; TRANSCRIPTOMICS; WEB BROWSER;

ANIMALS; DATABASES, GENETIC; DIABETES MELLITUS, TYPE 1; GENE EXPRESSION; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HEMATOPOIETIC STEM CELLS; HUMANS; MICE; RATS; SOFTWARE;

RATTUS;

EID: 78651275599     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq912     Document Type: Article

References (34)

1. Todd,J.A.(2010) Etiology of type 1 diabetes. Immunity, 32, 457-467.
2. Barrett,J.C., Clayton,D.G., Concannon,P., Akolkar,B., Cooper,J.D., Erlich,H.A., Julier,C., Morahan,G., Nerup,J., Nierras,C. et al. (2009) Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes. Nat. Genet., 41, 703-707.
3. Cooper,J.D., Smyth,D.J., Smiles,A.M., Plagnol,V., Walker,N.M., Allen,J.E., Downes,K., Barrett,J.C., Healy,B.C., Mychaleckyj,J.C. et al. (2008) Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci. Nat. Genet., 40, 1399-1401.
4. Wellcome Trust Case Control Consortium. (2007) Genome-wide association study of 14, 000 cases of seven common diseases and 3, 000 shared controls. Nature, 447, 661-678.
5. Qu,H.Q., Grant,S.F., Bradfield,J.P., Kim,C., Frackelton,E., Hakonarson,H. and Polychronakos,C.(2009) Association of RASGRP1 with type 1 diabetes is revealed by combined follow-up of two genome-wide studies. J. Med. Genet., 46, 553-554.
6. 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.
7. Smyth,D.J., Plagnol,V., Walker,N.M., Cooper,J.D., Downes,K., Yang,J.H., Howson,J.M., Stevens,H., McManus,R., Wijmenga,C. et al. (2008) Shared and distinct genetic variants in type 1 diabetes and celiac disease. N. Engl. J. Med., 359, 2767-2777.
8. Ridgway,W.M., Peterson,L.B., Todd,J.A., Rainbow,D.B., Healy,B., Burren,O.S. and Wicker,L.S.(2008) In Emil,R.U. and Hugh,O.M.(eds), Advances in Immunology, Vol. 100. Academic Press, pp. 151-175.
9. Wallis,R.H., Wang,K., Marandi,L., Hsieh,E., Ning,T., Chao,G.Y., Sarmiento,J., Paterson,A.D. and Poussier,P.(2009) Type 1 diabetes in the BB rat: A polygenic disease. Diabetes, 58, 1007-1017.
10. Kutlu,B., Burdick,D., Baxter,D., Rasschaert,J., Flamez,D., Eizirik,D.L., Welsh,N., Goodman,N. and Hood,L.(2009) Detailed transcriptome atlas of the pancreatic beta cell. BMC Med Genomics, 2, 3.
11. Watkins,N.A., Gusnanto,A., de Bono,B., De,S., Miranda- Saavedra,D., Hardie,D.L., Angenent,W.G., Attwood,A.P., Ellis,P.D., Erber,W. et al. (2009) A HaemAtlas: Characterizing gene expression in differentiated human blood cells. Blood, 113, e1-e9.
12. Hubbard,T.J., Aken,B.L., Ayling,S., Ballester,B., Beal,K., Bragin,E., Brent,S., Chen,Y., Clapham,P., Clarke,L. et al. (2009) Ensembl 2009. Nucleic Acids Res., 37, D690-D697.
13. Wheeler,D.L., Barrett,T., Benson,D.A., Bryant,S.H., Canese,K., Chetvernin,V., Church,D.M., DiCuccio,M., Edgar,R., Federhen,S. et al. (2007) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 35, D5-D12.
14. Bult,C.J., Eppig,J.T., Kadin,J.A., Richardson,J.E. and Blake,J.A.(2008) The Mouse Genome Database (MGD): Mouse biology and model systems. Nucleic Acids Res., 36, D724-D728.
15. Twigger,S.N., Shimoyama,M., Bromberg,S., Kwitek,A.E. and Jacob,H.J.(2007) The Rat Genome Database, update 2007: Easing the path from disease to data and back again. Nucleic Acids Res., 35, D658-D662.
16. Chen,F., Mackey,A.J., Stoeckert,C.J.Jr and Roos,D.S.(2006) OrthoMCL-DB: Querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res., 34, D363-D368.
17. Rhead,B., Karolchik,D., Kuhn,R.M., Hinrichs,A.S., Zweig,A.S., Fujita,P.A., Diekhans,M., Smith,K.E., Rosenbloom,K.R., Raney,B.J. et al. (2010) The UCSC Genome Browser database: Update 2010. Nucleic Acids Res., 38, D613-D619.
18. Pruitt,K.D., Harrow,J., Harte,R.A., Wallin,C., Diekhans,M., Maglott,D.R., Searle,S., Farrell,C.M., Loveland,J.E., Ruef,B.J. et al. (2009) The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res., 19, 1316-1323.
19. Sherry,S.T., Ward,M.H., Kholodov,M., Baker,J., Phan,L., Smigielski,E.M. and Sirotkin,K.(2001) dbSNP: The NCBI database of genetic variation. Nucleic Acids Res., 29, 308-311.
20. Stein,L.D., Mungall,C., Shu,S., Caudy,M., Mangone,M., Day,A., Nickerson,E., Stajich,J.E., Harris,T.W., Arva,A. et al. (2002) The generic genome browser: A building block for a model organism system database. Genome Res., 12, 1599-1610.
21. Smedley,D., Haider,S., Ballester,B., Holland,R., London,D., Thorisson,G. and Kasprzyk,A.(2009) BioMart-biological queries made easy. BMC Genomics, 10, 22.
22. Wallace,C., Smyth,D.J., Maisuria-Armer,M., Walker,N.M., Todd,J.A. and Clayton,D.G.(2010) The imprinted DLK1-MEG3 gene region on chromosome 14q32.2 alters susceptibility to type 1 diabetes. Nat. Genet., 42, 68-71.
23. Homer,N., Szelinger,S., Redman,M., Duggan,D., Tembe,W., Muehling,J., Pearson,J.V., Stephan,D.A., Nelson,S.F. and Craig,D.W.(2008) Resolving individuals contributing trace amounts of DNA to highly complex mixtures using high-density SNP genotyping microarrays. PLoS Genet., 4, e1000167.
24. Frazer,K.A., Ballinger,D.G., Cox,D.R., Hinds,D.A., Stuve,L.L., Gibbs,R.A., Belmont,J.W., Boudreau,A., Hardenbol,P., Leal,S.M. et al. (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature, 449, 851-U853.
25. R Core Development Team. (2005) R: A Language and Environment for Statistical Computing, Vienna, Austria.
26. Clayton,D. and Leung,H.T.(2007) An R package for analysis of whole-genome association studies. Hum. Hered., 64, 45-51.
27. Gentleman,R.C., Carey,V.J., Bates,D.M., Bolstad,B., Dettling,M., Dudoit,S., Ellis,B., Gautier,L., Ge,Y., Gentry,J. et al. (2004) Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol., 5, R80.
28. Smyth,G.K. (2005) Limma: Linear models for microarray data. In Gentleman,R., Carey,V., Dudoit,S., Irizarry,R. and Huber,W. (eds), Bioinformatics and Computational Biology Solutions using R and Bioconductor. Springer, New York, pp. 397-420.
29. Kent,W.J.(2002) BLAT: The BLAST-like alignment tool. Genome Res., 12, 656-664.
30. Heap,G.A., Yang,J.H., Downes,K., Healy,B.C., Hunt,K.A., Bockett,N., Franke,L., Dubois,P.C., Mein,C.A., Dobson,R.J. et al. (2010) Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing. Hum. Mol. Genet., 19, 122-134.
31. Zeller,T., Wild,P., Szymczak,S., Rotival,M., Schillert,A., Castagne,R., Maouche,S., Germain,M., Lackner,K., Rossmann,H. et al. (2010) Genetics and beyond-the transcriptome of human monocytes and disease susceptibility. PLoS ONE, 5, e10693.
32. Degner,J.F., Marioni,J.C., Pai,A.A., Pickrell,J.K., Nkadori,E., Gilad,Y. and Pritchard,J.K.(2009) Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics, 25, 3207-3212.
33. Dowell,R.D., Jokerst,R.M., Day,A., Eddy,S.R. and Stein,L.(2001) The distributed annotation system. BMC Bioinformatics, 2, 7.
34. Kent,W.J., Zweig,A.S., Barber,G., Hinrichs,A.S. and Karolchik,D.(2010) BigWig and BigBed: Enabling browsing of large distributed datasets. Bioinformatics, 26, 2204-2207.