ANEXdb: an integrated animal ANnotation and microarray EXpression database
- 135 Downloads
To determine annotations of the sequence elements on microarrays used for transcriptional profiling experiments in livestock species, currently researchers must either use the sparse direct annotations available for these species or create their own annotations. ANEXdb (http://www.anexdb.org) is an open-source web application that supports integrated access of two databases that house microarray expression (ExpressDB) and EST annotation (AnnotDB) data. The expression database currently supports storage and querying of Affymetrix-based expression data as well as retrieval of experiments in a form ready for NCBI-GEO submission; these services are available online. AnnotDB currently houses a novel assembly of approximately 1.6 million unique porcine-expressed sequence reads called the Iowa Porcine Assembly (IPA), which consists of 140,087 consensus sequences, the Iowa Tentative Consensus (ITC) sequences, and 103,888 singletons. The IPA has been annotated via transfer of information from homologs identified through sequence alignment to NCBI RefSeq. These annotated sequences have been mapped to the Affymetrix porcine array elements, providing annotation for 22,569 of the 23,937 (94%) porcine-specific probe sets, of which 19,253 (80%) are linked to an NCBI RefSeq entry. The ITC has also been mined for sequence variation, providing evidence for up to 202,383 SNPs, 62,048 deletions, and 958 insertions in porcine-expressed sequence. These results create a single location to obtain porcine annotation of and sequence variation in differently expressed genes in expression experiments, thus permitting possible identification of causal variants in such genes of interest. The ANEXdb application is open source and available from SourceForge.net.
KeywordsMinor Allele RefSeq Database NCBI RefSeq Porcine Sequence Minor Allele Count
We thank the USDA CSREES-NRI-2005-3560415618 and the ISU Center for Integrated Animal Genomics for funding this project. A USDA MGET 2001-52100-11506 Fellowship to O.C. is gratefully acknowledged. KC was funded under a NIH-NSF BBSI-0234102 award to Iowa State University.
- Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (2000) Basic local alignment search tool. J Mol Biol 215:403–410Google Scholar
- Ernst CW, Steibel JP, Ramos AM, Lunney JK, Wysocki M et al (2008) Assessment of the swine protein-annotated oligonucleotide microarray and utility of the arrays for eQTL and transcriptional profiling studies. Plant and Animal Genome XVI, San Diego, CA, 12–16 January 2008, pp W494Google Scholar