BioGPS and GXD: Mouse gene expression data-the benefits and challenges of data integration

Mammalian Genome

Volumn 23, Issue 9-10, 2012, Pages 550-558

  Ringwald, Martin ^a   Wu, Chunlei ^b   Su, Andrew I ^b  

^a JACKSON LABORATORY   (United States)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ALLELE; ARTICLE; DATA EXTRACTION; GENE EXPRESSION; GENE IDENTIFICATION; GENE LIBRARY; GENE MAPPING; GENETIC DATABASE; GENETIC MODEL; GENETIC RESOURCE; GENETIC SCREENING; GENOME ANALYSIS; IMAGE ANALYSIS; INFORMATION DISSEMINATION; INFORMATION RETRIEVAL; MOLECULAR IMAGING; MOUSE; NONHUMAN; ONLINE SYSTEM; PHENOTYPE;

ANIMALS; DATABASES, GENETIC; GENE EXPRESSION; INFORMATION STORAGE AND RETRIEVAL; MICE;

EID: 84867336782     PISSN: 09388990     EISSN: 14321777     Source Type: Journal    
DOI: 10.1007/s00335-012-9408-0     Document Type: Article

References (35)

1. Bard JB, Kaufman MH, Dubreuil C, Brune RM, Burger A, Baldock RA, Davidson DR (1998) An internet-accessible database of mouse developmental anatomy based on a systematic nomenclature. Mech Dev 74:111-120
2. Barrett T, Troup DB, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall AK, Phillippy KH, Sherman PM, Muertter RN, Holko M, Ayanbule O, Yefanov A, Soboleva A (2011) NCBI GEO: archive for functional genomics data sets-10 years on. Nucleic Acids Res 39:D1005-D1010
3. Belleau F, Nolin MA, Tourigny N, Rigault P, Morissette J (2008) Bio2RDF: towards a mashup to build bioinformatics knowledge systems. J Biomed Inform 41(5):706-716
4. Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FCP, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M (2001) Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 29:365-371
5. Diez-Roux G, Banfi S, Sultan M, Geffers L, Anand S et al (2011) A high-resolution anatomical atlas of the transcriptome in the mouse embryo. PLoS Biol 9(1):e1000582
6. ENCODE Project Consortium (2011) A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol 9(4):e1001046
7. Eppig JT, Blake JA, Bult CJ, Kadin JA, Richardson JE, the Mouse Genome Database Group (2012) The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse. Nucleic Acids Res 40(1):D881-D886
8. Finger JH, Smith CM, Hayamizu TF, McCright IJ, Eppig JT, Kadin JA, Richardson JE, Ringwald M (2011) The mouse Gene Expression Database (GXD): 2011 update. Nucleic Acids Res 39(1):D835-D841
9. Gates H, Mallon AM, Brown SD, EUMODIC Consortium (2011) High-throughput mouse phenotyping. Methods 53(4):394-404
10. Haendel MA, Gkoutos GV, Lewis SE, Mungall CJ (2009) Uberon: towards a comprehensive multi-species anatomy ontology. Presented at the International Conference on Biomedical Ontology (ICBO), 26 July 2009. Available at Nature Precedings, http://precedings.nature.com/documents/3592/version/1
11. Hayamizu TF, Mangan M, Corradi JP, Kadin JA, Ringwald M (2005) The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data. Genome Biol 6:R29
12. Hayamizu TF, de Coronado S, Fragoso G, Sioutos N, Kadin JA, Ringwald M (2012) The mouse-human anatomy ontology mapping project. Database (Oxford) 2012:bar066
13. Hornshoj H, Conley LN, Hedegaard J, Sorensen P, Panitz F, Bendixen C (2007) Microarray expression profiles of 20, 000 genes across 23 healthy porcine tissues. PLoS One 11:e1203
14. Lattin JE, Schroder K, Su AI, Walker JR, Zhang J, Wiltshire T, Saijo K, Ck Glass, Hume DA, Kellie S, Sweet MJ (2008) Expression analysis of G protein-coupled receptors in mouse macrophages. Immunome Res 4:5
15. Lein ES, Hawrylycz MJ, Ao N, Ayres M, Bensinger A, Bernard A, Boe AF, Boguski MS, Brockway KS, Byrnes EJ et al (2007) Genome-wide atlas of gene expression in the adult mouse brain. Nature 445:168-176
16. Leipzig J, Pevzner P, Heber S (2004) The Alternative Splicing Gallery (ASG): bridging the gap between genome and transcriptome. Nucleic Acids Res 32:3977-3983
17. Magdaleno S, Jensen P, Brumwell CL, Seal A, Lehman K, Asbury A, Cheung T, Cornelius T, Batten DM, Eden C, Norland SM, Rice DS, Dosooye N, Shakya S, Mehta P, Curran T (2006) BGEM: an in situ hybridization database of gene expression in the embryonic and adult mouse nervous system. PLoS Biol 4:e86
18. McMahon AP, Aronow BJ, Davidson DR, Davies JA, Gaido KW, Grimmond S, Lessard JL, Little MH, Potter SS, Wilder EL, Zhang P, GUDMAP Project (2008) GUDMAP: the genitourinary developmental molecular anatomy project. J Am Soc Nephrol 19:667-671
19. Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B, NCBO team (2012) The National Center for Biomedical Ontology. J Am Med Inform Assoc 19:190-195
20. Oakley DJ, Iyer V, Skarnes WC, Smedley D (2011) BioMart as an integration solution for the International Knockout Mouse Consortium. Database (Oxford) 2011:bar028
21. Parkinson H, Sarkans U, Kolesnikov N, Abeygunawardena N, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Holloway E, Kurbatova N, Lukk M, Malone J, Mani R, Pilicheva E, Rustici G, Sharma A, Williams E, Adamusiak T, Brandizi M, Sklyar N, Brazma A (2011) ArrayExpress update-an archiveofmicroarray and high-throughput sequencing-based functional genomics experiments. Nucleic Acids Res 39:D1002-D1004
22. Rayner TF, Rocca-Serra P, Spellman PT, Causton HC, Farne A, Holloway E, Irizarry RA, Liu J, Maier DS, Miller M, Petersen K, Quackenbush J, Sherlock G, Christian J, Stoeckert CJ, White J, Whetzel PL, Wymore F, Parkinson H, Sarkans U, Catherine A, Ball CA, Brazma A (2006) A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinformatics 7:489
23. Richardson L, Venkataraman S, Stevenson P, Yang Y, Burton N, Rao J, Fisher M, Baldock RA, Davidson DR, Christiansen JH (2010) EMAGE mouse embryo spatial gene expression database: 2010 update. Nucleic Acids Res 38:D703-D709
24. Ringwald M, Baldock R, Bard J, Kaufman M, Eppig JT, Richardson JE, Nadeau JH, Davidson D (1994) A database for mouse development. Science 265:2033-2034
25. Ringwald M, Iyer V, Mason JC, Stone KR, Tadepally HD, Kadin JA, Bult CJ, Eppig JT, Oakley DJ, Briois S, Stupka E, Maselli V, Smedley D, Liu S, Hansen J, Baldock R, Hicks GG, Skarnes WC (2011) The IKMC web portal: a central point of entry to data and resources from the International Knockout Mouse Consortium. Nucleic Acids Res 39(1):D849-D855
26. Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, The OBI Consortium, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S (2007a) The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 25:1251-1255
27. Smith CM, Finger JH, Hayamizu TF, McCright IJ, Eppig JT, Kadin JA, Richardson JE, Ringwald M (2007b) The mouse Gene Expression Database (GXD): 2007 update. Nucleic Acids Res 35:D618-D623
28. Son CG, Bilke S, Davis S, Greer BT, Wei JS, Whiteford CC, Chen QR, Cenacchi N, Khan J (2005) Databaseof mRNA gene expression of profiles of multiple human organs. Genome Res 15(3):443-450
29. Splendiani A (2008) RDFScape: Semantic Web meets systems biology. BMC Bioinformatics 9(Suppl 4):S6
30. Stevenson P, Richardson L, Venkataraman S, Yang Y, Baldock R (2011) The BioMart interface to the eMouseAtlas gene expression database EMAGE. Database (Oxford) 2011:bar029
31. Su AI, Cooke MP, Ching KA, Hakak Y, Walker JR, Wiltshire T, Orth AP, Vega RG, Sapinoso LM, Moqrich A, Patapoutian A, Hampton GM, Schultz PG, Hogenesch JB (2002) Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci USA 99:4465-4470
32. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, Cooke MP, Walker JR, Hogenesch JB (2004) A gene atlas of the mouse human proteinencoding transcriptomes. Proc Natl Acad Sci USA 101:6062-6067
33. Visel A, Thaller C, Eichele G (2004) GenePaint.org: an atlas of gene expression patterns in the mouse embryo. Nucleic Acids Res 32:D552-D556
34. Walker JR, Su AI, Self DW, Hogenesch JB, Lapp H, Maier R, Hoyer D, Bilbe G (2004) Applications of a rat multiple tissue gene expression data set. Genome Res 14(4):742-749
35. Wu C, Orozco C, Boyer J, Leglise M, Goodale J, Batalov S, Hodge CL, Haase J, Janes J, Huss JW, Su AI (2009) BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. Genome Biol 10:R130