Facilitating functional annotation of chicken microarray data

BMC Bioinformatics

Volumn 10, Issue SUPPL. 11, 2009, Pages

  Buza, Teresia J ^a,b   Kumar, Ranjit ^a,b   Gresham, Cathy R ^b,d   Burgess, Shane C ^a,b,c   McCarthy, Fiona M ^a,b  

^a MISSISSIPPI STATE UNIVERSITY   (United States)

^b MISSISSIPPI STATE UNIVERSITY   (United States)

^c MISSISSIPPI STATE UNIVERSITY   (United States)

^d MISSISSIPPI STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DISEASE CONTROL; GENES;

COMPLEX BIOLOGICAL SYSTEMS; DRUG DISCOVERY; FUNCTIONAL ANNOTATION; FUNCTIONAL GENOMICS; FUNCTIONAL INFORMATION; MICROARRAY DATA; MICROARRAY DATASET; RESEARCH TOOLS;

ANIMALS;

ARTICLE; BIRD DISEASE; CHICKEN; DRUG TARGETING; FUNCTIONAL GENOMICS; GENE IDENTIFICATION; GENETIC DATABASE; INFORMATION RETRIEVAL; MICROARRAY ANALYSIS; SEARCH ENGINE;

EID: 70449434792     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-S11-S2     Document Type: Article

References (22)

1. Heidari M, Huebner M, Kireev D, Silva RF. Transcriptional profiling of Marek's disease virus genes during cytolytic and latent infection. Virus Genes 2008, 36(2):383-392. 10.1007/s11262-008-0203-7, 18266100.
2. Sarson AJ, Read LR, Haghighi HR, Lambourne MD, Brisbin JT, Zhou H, Sharif S. Construction of a microarray specific to the chicken immune system: profiling gene expression in B cells after lipopolysaccharide stimulation. Can J Vet Res 2007, 71(2):108-118. 1829180, 17479774.
3. Smith J, Speed D, Hocking PM, Talbot RT, Degen WG, Schijns VE, Glass EJ, Burt DW. Development of a chicken 5 K microarray targeted towards immune function. BMC Genomics 2006, 7:49. 1440325, 16533398, 10.1186/1471-2164-7-49.
4. Masker K, Golden A, Gaffney CJ, Mazack V, Schwindinger WF, Zhang W, Wang LH, Carey DJ, Sudol M. Transcriptional profile of Rous Sarcoma Virus transformed chicken embryo fibroblasts reveals new signaling targets of viral-src. Virology 2007, 364(1):10-20. 1974879, 17448514, 10.1016/j.virol.2007.03.026.
5. Clark TA, Schweitzer AC, Chen TX, Staples MK, Lu G, Wang H, Williams A, Blume JE. Discovery of tissue-specific exons using comprehensive human exon microarrays. Genome Biol 2007, 8(4):R64. 1896007, 17456239, 10.1186/gb-2007-8-4-r64.
6. Grigoryev DN, Ma SF, Shimoda LA, Johns RA, Lee B, Garcia JG. Exon-based mapping of microarray probes: recovering differential gene expression signal in underpowered hypoxia experiment. Mol Cell Probes 2007, 21(2):134-139. 1852466, 17071053, 10.1016/j.mcp.2006.09.002.
7. Xing Y, Kapur K, Wong WH. Probe selection and expression index computation of Affymetrix Exon Arrays. PLoS ONE 2006, 1:e88. 1762343, 17183719, 10.1371/journal.pone.0000088.
8. Cao W, Epstein C, Liu H, DeLoughery C, Ge N, Lin J, Diao R, Cao H, Long F, Zhang X. Comparing gene discovery from Affymetrix GeneChip microarrays and Clontech PCR-select cDNA subtraction: a case study. BMC Genomics 2004, 5(1):26. 415544, 15113399, 10.1186/1471-2164-5-26.
9. Butcher LM, Meaburn E, Liu L, Fernandes C, Hill L, Al-Chalabi A, Plomin R, Schalkwyk L, Craig IW. Genotyping pooled DNA on microarrays: a systematic genome screen of thousands of SNPs in large samples to detect QTLs for complex traits. Behav Genet 2004, 34(5):549-555. 10.1023/B:BEGE.0000038493.26202.d3, 15319578.
10. Meaburn E, Butcher LM, Liu L, Fernandes C, Hansen V, Al-Chalabi A, Plomin R, Craig I, Schalkwyk LC. Genotyping DNA pools on microarrays: tackling the QTL problem of large samples and large numbers of SNPs. BMC Genomics 2005, 6(1):52. 1079828, 15811185, 10.1186/1471-2164-6-52.
11. Corless CE, Kaczmarski E, Borrow R, Guiver M. Molecular characterization of Neisseria meningitidis isolates using a resequencing DNA microarray. J Mol Diagn 2008, 10(3):265-271. 2329792, 18372424, 10.2353/jmoldx.2008.070152.
12. Lebet T, Chiles R, Hsu AP, Mansfield ES, Warrington JA, Puck JM. Mutations causing severe combined immunodeficiency: detection with a custom resequencing microarray. Genet Med 2008, 10(8):575-585.
13. Chung HR, Kostka D, Vingron M. A physical model for tiling array analysis. Bioinformatics 2007, 23(13):i80-86. 10.1093/bioinformatics/btm167, 17646349.
14. Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Marshall KA. NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res 2009, (37 Database):D885-890. 2686538, 18940857, 10.1093/nar/gkn764.
15. Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 2002, 30(1):207-210. 99122, 11752295, 10.1093/nar/30.1.207.
16. Zhu Y, Davis S, Stephens R, Meltzer PS, Chen Y. GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus. Bioinformatics 2008, 24(23):2798-2800. 2639278, 18842599, 10.1093/bioinformatics/btn520.
17. GeneChip® Arrays: Chicken Genome Array. [http://www.affymetrix.com/technology/index.affx, http://www.affymetrix.com/products/arrays/specific/chicken.affx].
18. Liu G, Loraine AE, Shigeta R, Cline M, Cheng J, Valmeekam V, Sun S, Kulp D, Siani-Rose MA. NetAffx: Affymetrix probesets and annotations. Nucleic Acids Res 2003, 31(1):82-86. 165568, 12519953, 10.1093/nar/gkg121.
19. Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 2004, (32 Database):D258-261. 308770, 14681407.
20. Buza TJ, McCarthy FM, Wang N, Bridges SM, Burgess SC. Gene Ontology annotation quality analysis in model eukaryotes. Nucleic Acids Res 2008, 36(2):e12. 2241866, 18187504, 10.1093/nar/gkm1167.
21. Rhee SY, Wood V, Dolinski K, Draghici S. Use and misuse of the gene ontology annotations. Nat Rev Genet 2008, 9(7):509-515. 10.1038/nrg2363, 18475267.
22. McCarthy FM, Bridges SM, Wang N, Magee GB, Williams WP, Luthe DS, Burgess SC. AgBase: a unified resource for functional analysis in agriculture. Nucleic Acids Res 2007, (35 Database):D599-603. 1751552, 17135208, 10.1093/nar/gkl936.