ANEXdb: an integrated animal ANnotation and microarray EXpression database.

Mammalian Genome : Official Journal of the International Mammalian Genome Society
Oliver P CoutureChristopher K Tuggle

Abstract

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 (...Continue Reading

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Citations

Nov 8, 2011·Basic Research in Cardiology·Diederik W D KusterDirk J Duncker
May 31, 2011·American Journal of Physiology. Heart and Circulatory Physiology·Jaume PadillaM Harold Laughlin
Dec 3, 2014·Journal of Molecular and Cellular Cardiology·Diederik W D KusterDirk J Duncker
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Apr 18, 2013·Physiological Genomics·Jaume PadillaR Scott Rector
Mar 7, 2012·The Journal of Immunology : Official Journal of the American Association of Immunologists·Ronan KapetanovicDavid A Hume

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