Facilitating functional annotation of chicken microarray data

作者: Teresia J Buza , Ranjit Kumar , Cathy R Gresham , Shane C Burgess , Fiona M McCarthy

DOI: 10.1186/1471-2105-10-S11-S2

关键词:

摘要: Modeling results from chicken microarray studies is challenging for researchers due to little functional annotation associated with these arrays. The Affymetrix GenChip genome array, one of the biggest arrays that serve as a key research tool study genomics, among few link gene products Gene Ontology (GO). However GO data presented by incomplete, example, they do not show references linked manually annotated functions. In addition, there no facilitates directly retrieve annotations their datasets This costs amount time in searching multiple databases information. We have improved breadth probesets on array 45% and quality 14%. also identified most significant diseases disorders, different types genes, known drug targets represented array. To facilitate other experimental we developed an Array Mapper (AGOM) help quickly corresponding information dataset. Results this will datasets. Researchers be able model dataset into more reliable biological using AGOM tool. disease, revealed allow learn about how genes function complex systems may lead new discovery development therapies. generated available public use via AgBase website updated regular basis.

参考文章(21)
Melissa D. Lambourne, Jennifer T. Brisbin, Hamid R. Haghighi, Shayan Sharif, Huaijun Zhou, Aimie J. Sarson, Leah R. Read, Construction of a microarray specific to the chicken immune system: profiling gene expression in B cells after lipopolysaccharide stimulation. Canadian Journal of Veterinary Research-revue Canadienne De Recherche Veterinaire. ,vol. 71, pp. 108- 118 ,(2007)
Gene Ontology Consortium, None, The Gene Ontology (GO) database and informatics resource Nucleic Acids Research. ,vol. 32, pp. 258D- 261 ,(2004) , 10.1093/NAR/GKH036
Emma Meaburn, Lee M Butcher, Lin Liu, Cathy Fernandes, Valerie Hansen, Ammar Al-Chalabi, Robert Plomin, Ian Craig, Leonard C Schalkwyk, Genotyping DNA pools on microarrays: Tackling the QTL problem of large samples and large numbers of SNPs BMC Genomics. ,vol. 6, pp. 52- 52 ,(2005) , 10.1186/1471-2164-6-52
Jacqueline Smith, David Speed, Paul M Hocking, Richard T Talbot, Winfried GJ Degen, Virgil EJC Schijns, Elizabeth J Glass, David W Burt, Development of a chicken 5 K microarray targeted towards immune function. BMC Genomics. ,vol. 7, pp. 49- 49 ,(2006) , 10.1186/1471-2164-7-49
Dmitry N. Grigoryev, Shwu-Fan Ma, Larissa A. Shimoda, Roger A. Johns, Byungkook Lee, Joe G.N. Garcia, Exon-based mapping of microarray probes: Recovering differential gene expression signal in underpowered hypoxia experiment Molecular and Cellular Probes. ,vol. 21, pp. 134- 139 ,(2007) , 10.1016/J.MCP.2006.09.002
Lee M. Butcher, Emma Meaburn, Lin Liu, Cathy Fernandes, Linzy Hill, Ammar Al-Chalabi, Robert Plomin, Leo Schalkwyk, Ian W. Craig, Genotyping pooled DNA on microarrays: a systematic genome screen of thousands of SNPs in large samples to detect QTLs for complex traits. Behavior Genetics. ,vol. 34, pp. 549- 555 ,(2004) , 10.1023/B:BEGE.0000038493.26202.D3
Mohammad Heidari, Marianne Huebner, Dmitry Kireev, Robert F. Silva, Transcriptional profiling of Marek's disease virus genes during cytolytic and latent infection. Virus Genes. ,vol. 36, pp. 383- 392 ,(2008) , 10.1007/S11262-008-0203-7
Ron Edgar, Michael Domrachev, Alex E Lash, Gene Expression Omnibus: NCBI gene expression and hybridization array data repository Nucleic Acids Research. ,vol. 30, pp. 207- 210 ,(2002) , 10.1093/NAR/30.1.207
Seung Yon Rhee, Valerie Wood, Kara Dolinski, Sorin Draghici, Use and misuse of the gene ontology annotations Nature Reviews Genetics. ,vol. 9, pp. 509- 515 ,(2008) , 10.1038/NRG2363
Caroline E. Corless, Edward Kaczmarski, Ray Borrow, Malcolm Guiver, Molecular Characterization of Neisseria meningitidis Isolates Using a Resequencing DNA Microarray The Journal of Molecular Diagnostics. ,vol. 10, pp. 265- 271 ,(2008) , 10.2353/JMOLDX.2008.070152