Functional modelling of an equine bronchoalveolar lavage fluid proteome provides experimental confirmation and functional annotation of equine genome sequences

Animal Genetics

Volumn 42, Issue 4, 2011, Pages 395-405

  Bright, L A ^a,b   Mujahid, N ^a   Nanduri, B ^a,b   McCarthy, F M ^a,b   Costa, L R R ^c   Burgess, S C ^a,b,d   Swiderski, C E ^a,b  

^a MISSISSIPPI STATE UNIVERSITY   (United States)

^b MISSISSIPPI STATE UNIVERSITY   (United States)

^c TUFTS UNIVERSITY   (United States)

^d MISSISSIPPI STATE UNIVERSITY   (United States)

Author keywords

bronchoalveolar lavage; equine; genome annotation; proteomics

Indexed keywords

PROTEIN;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; CHEMISTRY; COMPARATIVE STUDY; GENETICS; GENOME; HORSE; HUMAN; LUNG LAVAGE; MASS SPECTROMETRY; METHODOLOGY; MOLECULAR GENETICS; MOUSE; PHYSIOLOGY; PROTEOMICS;

ANIMALS; BRONCHOALVEOLAR LAVAGE FLUID; GENOME; HORSES; HUMANS; MASS SPECTROMETRY; MICE; MODELS, BIOLOGICAL; MOLECULAR SEQUENCE ANNOTATION; PROTEINS; PROTEOMICS;

EQUIDAE;

EID: 79960363654     PISSN: 02689146     EISSN: 13652052     Source Type: Journal    
DOI: 10.1111/j.1365-2052.2010.02158.x     Document Type: Article

References (27)

1. Bright L.A., Burgess S.C., Chowdhary B., Swiderski C.E., &, McCarthy F.M., (2009) Structural and functional-annotation of an equine whole genome oligoarray. BMC Bioinformatics 10 (Suppl. 11), S8.
2. Burrell M.H., Wood J.L., Whitwell K.E., Chanter N., Mackintosh M.E., &, Mumford J.A., (1996) Respiratory disease in thoroughbred horses in training: the relationships between disease and viruses, bacteria and environment. Veterinary Record 139, 308-13. (Pubitemid 126614389)
3. Camon E., Magrane M., Barrell D., et al. (2003) The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro. Genome Research 13, 662-72. (Pubitemid 36511925)
4. Chen F., Mackey A.J., Stoeckert C.J. Jr, &, Roos D.S., (2006) OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Research 34, D363-8.
5. Chen J., Ryu S., Gharib S.A., Goodlett D.R., &, Schnapp L.M., (2008) Exploration of the normal human bronchoalveolar lavage fluid proteome. Proteomics: Clinical Applications 2, 585-95. (Pubitemid 351566265)
6. Cheng J., Sun S., Tracy A., et al. (2004) NetAffx Gene Ontology Mining Tool: a visual approach for microarray data analysis. Bioinformatics 20, 1462-3. (Pubitemid 38931419)
7. Costa L.R.R., Eades S.C., Venugopal S.S., &, Moore R.M., (2009) Plasma and Pulmonary Fluid Endothelin in Horses with Seasonal Recurrent Airway Obstruction. Journal of Veterinary internal Medicine. 23, 1239-46.
8. Durinck S., Moreau Y., Kasprzyk A., Davis S., De Moor B., Brazma A., &, Huber W., (2005) BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics 21, 3439-40. (Pubitemid 41222455)
9. Gerling I.C., Singh S., Lenchik N.I., Marshall D.R., &, Wu J., (2006) New data analysis and mining approaches identify unique proteome and transcriptome markers of susceptibility to autoimmune diabetes. Molecular & Cellular Proteomics 5, 293-305. (Pubitemid 43329307)
10. Guo Y., Ma S.F., Grigoryev D., Van Eyk J., &, Garcia J.G., (2005) 1-DE MS and 2-D LC-MS analysis of the mouse bronchoalveolar lavage proteome. Proteomics 5, 4608-24. (Pubitemid 41739938)
11. Huang Y., Yan J., Lubet R., Kensler T.W., &, Sutter T.R., (2006) Identification of novel transcriptional networks in response to treatment with the anticarcinogen 3H-1,2-dithiole-3-thione. Physiological Genomics 24, 144-53.
12. Hubbard T.J., Aken B.L., Beal K., et al. (2007) Ensembl 2007. Nucleic Acids Research 35, D610-7. (Pubitemid 46056279)
13. Hulsen T., Huynen M.A., de Vlieg J., &, Groenen P.M., (2006) Benchmarking ortholog identification methods using functional genomics data. Genome Biology 7, R31.
14. Lewis S., Ashburner M., &, Reese M.G., (2000) Annotating eukaryote genomes. Current Opinion in Structural Biology 10, 349-54. (Pubitemid 30333106)
15. Li L., Stoeckert C.J. Jr, &, Roos D.S., (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Research 13, 2178-89. (Pubitemid 37161775)
16. Li H., Coghlan A., Ruan J., et al. (2006) TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Research 34, D572-80.
17. Maglott D., Ostell J., Pruitt K.D., &, Tatusova T., (2007) Entrez Gene: gene-centered information at NCBI. Nucleic Acids Research 35, D26-31. (Pubitemid 46056164)
18. Martens L., Hermjakob H., Jones P., Adamski M., Taylor C., States D., Gevaert K., Vandekerckhove J., &, Apweiler R., (2005) PRIDE: the proteomics identifications database. Proteomics 5, 3537-45. (Pubitemid 41192059)
19. McCarthy F.M., Cooksey A.M., Wang N., Bridges S.M., Pharr G.T., &, Burgess S.C., (2006a) Modeling a whole organ using proteomics: the avian bursa of Fabricius. Proteomics 6, 2759-71.
20. McCarthy F.M., Wang N., Magee G.B., et al. (2006b) AgBase: a functional genomics resource for agriculture. BMC Genomics 7, 229.
21. O'Brien K.P., Westerlund I., &, Sonnhammer E.L., (2004) OrthoDisease: a database of human disease orthologs. Human Mutation 24, 112-9. (Pubitemid 39006590)
22. Pendarvis K., Kumar R., Burgess S.C., &, Nanduri B., (2009) An automated proteomic data analysis workflow for mass spectrometry. BMC Bioinformatics 10 (Suppl. 11), S17.
23. Remm M., Storm C.E., &, Sonnhammer E.L., (2001) Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. Journal of Molecular Biology 314, 1041-52. (Pubitemid 34073068)
24. Resource U.P., (2007) The Universal Protein Resource (UniProt). Nucleic Acids Research 35, D193-7.
25. Wade C.M., Giulotto E., Sigurdsson S., et al. (2009) Genome sequence, comparative analysis, and population genetics of the domestic horse. Science 326, 865-7.
26. Wheeler D.L., Barrett T., Benson D.A., et al. (2007) Database resources of the National Center for Biotechnology Information. Nucleic Acids Research 35, D5-12. (Pubitemid 46056160)
27. Wright M.W., &, Bruford E.A., (2006) Human and orthologous gene nomenclature. Gene 369, 1-6. (Pubitemid 43327325)