Simplified ontologies allowing comparison of developmental mammalian gene expression

Genome Biology

Volumn 8, Issue 10, 2007, Pages

  Kruger, Adele ^a   Hofmann, Oliver ^a   Carninci, Piero ^b,c   Hayashizaki, Yoshihide ^b,c   Hide, Winston ^a  

^a UNIVERSITY OF THE WESTERN CAPE   (South Africa)

^b RIKEN YOKOHAMA INSTITUTE   (Japan)

^c RIKEN   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA;

ARTICLE; BIOINFORMATICS; BRAIN DEVELOPMENT; CONTROLLED STUDY; DATA ANALYSIS; DATA MINING; DEVELOPMENTAL BIOLOGY; DNA LIBRARY; GENE EXPRESSION; GENE IDENTIFICATION; GENETIC DATABASE; MAMMAL; NEUROANATOMY; ORTHOLOGY; SPECIES DIFFERENCE; ANIMAL; BRAIN; COMPARATIVE STUDY; EMBRYO DEVELOPMENT; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE LIBRARY; GENETICS; HUMAN; METABOLISM; METHODOLOGY; MOUSE; NOMENCLATURE; PRENATAL DEVELOPMENT;

MAMMALIA;

ANIMALS; BRAIN; EMBRYONIC DEVELOPMENT; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE LIBRARY; HUMANS; MICE; SPECIES SPECIFICITY; TERMINOLOGY AS TOPIC;

EID: 42949166327     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2007-8-10-r229     Document Type: Article

References (30)

1. RIKEN Genomic Sciences Centre http://www.gsc.riken.go.jp/indexE.html
2. Gkoutos GV Green EC Mallon AM Hancock JM Davidson D Using ontologies to describe mouse phenotypes. Genome Biol 2005 6 R8 549069 15642100 10.1186/ gb-2004-6-1-r8
3. Bard J Winter R Ontologies of developmental anatomy: Their current and future roles. Brief Bioinform 2001 2 289-299 10.1093/bib/2.3.289 11589589
4. The Open Biomedical Ontologies http://obofoundry.org/
5. Baldock RA Bard JB Burger A Burton N Christiansen J Feng G Hill B Houghton D Kaufman M Rao J et al. EMAP and EMAGE: A framework for understanding spatially organized data. Neuroinformatics 2003 1 309-325 10.1385/NI:1:4:309 15043218
6. Hayamizu TF Mangan M Corradi JP Kadin JA Ringwald M The Adult Mouse Anatomical Dictionary: A tool for annotating and integrating data. Genome Biol 2005 6 R29 1088948 15774030 10.1186/gb-2005-6-3-r29
7. Hunter A Kaufman MH McKay A Baldock R Simmen MW Bard JB An ontology of human developmental anatomy. J Anat 2003 203 347-355 1571174 14620375 10.1046/j.1469-7580.2003.00224.x
8. Rosse C Mejino JLJ A reference ontology for biomedical informatics: The Foundational Model of Anatomy. J Biomed Inform 2003 36 478-500 10.1016/ j.jbi.2003.11.007 14759820
9. Parkinson H Aitken S Baldock RA Bard JBL Burger A Hayamizu TF Rector A Ringwald M Rogers J Rosse C et al. The SOFG anatomy entry list (SAEL): an annotation tool for functional genomics data. Comparative Functional Genomics 2004 5 521-527 10.1002/cfg.434
10. Martin D Brun C Remy E Mouren P Thieffry D Jacq B GOToolBox: Functional analysis of gene datasets based on Gene Ontology. Genome Biol 2004 5 R101 545796 15575967 10.1186/gb-2004-5-12-r101
11. Kelso J Visagie J Theiler G Christoffels A Bardien S Smedley D Otgaar D Greyling G Jongeneel CV McCarthy MI et al. eVOC: A controlled vocabulary for unifying gene expression data. Genome Res 2003 13 1222-1230 403650 12799354 10.1101/gr.985203
12. Marra M Hillier L Kucaba T Allen M Barstead R Beck C Blistain A Bonaldo M Bowers Y Bowles L et al. An encyclopedia of mouse genes. Nat Genet 1999 21 191-194 10.1038/5976 9988271
13. Lindsay S Copp AJ MRC-Wellcome Trust Human Developmental Biology Resource: Enabling studies of human developmental gene expression. Trends Genet 2005 21 586-590 10.1016/j.tig.2005.08.011 16154230
14. Magdaleno S Jensen P Brumwell CL Seal A Lehman K Asbury A Cheung T Cornelius T Batten DM Eden C et al. BGEM: An in situ hybridization database of gene expression in the embryonic and adult mouse nervous system. PLoS Biol 2006 4 e86 1413568 16602821 10.1371/ journal.pbio.0040086
15. Kho AT Zhao Q Cai Z Butte AJ Kim JY Pomeroy SL Rowitch DH Kohane IS Conserved mechanisms across development and tumorigenesis revealed by a mouse development perspective of human cancers. Genes Dev 2004 18 629-640 387239 15075291 10.1101/gad.1182504
16. Zhou XJ Gibson G Cross-species comparison of genome-wide expression patterns. Genome Biol 2004 5 232 463279 15239823 10.1186/gb-2004-5-7-232
17. Eilbeck K Lewis SE Mungall CJ Yandell M Stein L Durbin R Ashburner M The Sequence Ontology: A tool for the unification of genome annotations. Genome Biol 2005 6 R44 1175956 15892872 10.1186/gb-2005-6-5-r44
18. Dennis GJ Sherman BT Hosack DA Yang J Gao W Lane HC Lempicki RA DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 2003 4 P3 10.1186/gb-2003-4-5-p3 12734009
19. Carninci P Kasukawa T Katayama S Gough J Frith MC Maeda N Oyama R Ravasi T Lenhard B Wells C et al. The transcriptional landscape of the mammalian genome. Science 2005 309 1559-1563 10.1126/science.1112014 16141072
20. EHDA: Human Versus Mouse Development Stage Comparison http://www.ana.ed.ac.uk/anatomy/database/humat/MouseComp.html
21. Smith B Ceusters W Klagges B Kohler J Kumar A Lomax J Mungall C Neuhaus F Rector AL Rosse C Relations in biomedical ontologies. Genome Biol 2005 6 R46 1175958 15892874 10.1186/gb-2005-6-5-r46
22. The Cancer Genome Anatomy Project http://cgap.nci.nih.gov/
23. Odom DT Dowell RD Jacobsen ES Gordon W Danford TW Macisaac KD Rolfe PA Conboy CM Gifford DK Fraenkel E Tissue-specific transcriptional regulation has diverged significantly between human and mouse. Nat Genet 2007 39 730-732 10.1038/ng2047 17529977
24. Aitken S Korf R Webber B Bard J COBrA: A bio-ontology editor. Bioinformatics 2005 21 825-826 10.1093/bioinformatics/bti097 15513995
25. DAG-edit http://www.geneontology.org/GO.tools.shtml#dagedit
26. Ashburner M Ball CA Blake JA Botstein D Butler H Cherry JM Davis AP Dolinski K Dwight SS Eppig JT et al. Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000 25 25-29 10.1038/75556 10802651
27. Hill DP Begley DA Finger JH Hayamizu TF McCright IJ Smith CM Beal JS Corbani LE Blake JA Eppig JT et al. The mouse Gene Expression Database (GXD): Updates and enhancements. Nucleic Acids Res 2004 32 D568-571 308803 14681482 10.1093/nar/gkh069
28. NCBI UniGene http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene
29. NCBI HomoloGene http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db= homologene
30. eVOC ontology http://www.evocontology.org