Mammalian Genome

, Volume 20, Issue 11–12, pp 768–777

ANEXdb: an integrated animal ANnotation and microarray EXpression database

  • Oliver Couture
  • Keith Callenberg
  • Neeraj Koul
  • Sushain Pandit
  • Remy Younes
  • Zhi-Liang Hu
  • Jack Dekkers
  • James Reecy
  • Vasant Honavar
  • Christopher Tuggle
Article

DOI: 10.1007/s00335-009-9234-1

Cite this article as:
Couture, O., Callenberg, K., Koul, N. et al. Mamm Genome (2009) 20: 768. doi:10.1007/s00335-009-9234-1

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 (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.

Supplementary material

335_2009_9234_MOESM1_ESM.docx (70 kb)
Supplementary material 1 (DOCX 69 kb)

Copyright information

© Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Oliver Couture
    • 1
    • 2
  • Keith Callenberg
    • 2
    • 3
    • 4
  • Neeraj Koul
    • 5
  • Sushain Pandit
    • 5
  • Remy Younes
    • 5
  • Zhi-Liang Hu
    • 2
  • Jack Dekkers
    • 1
    • 2
    • 6
  • James Reecy
    • 1
    • 2
    • 6
  • Vasant Honavar
    • 5
    • 6
  • Christopher Tuggle
    • 1
    • 2
    • 6
  1. 1.Interdepartmental GeneticsIowa State UniversityAmesUSA
  2. 2.Department of Animal ScienceIowa State UniversityAmesUSA
  3. 3.Department of Computer ScienceSan Jose State UniversitySan JoseUSA
  4. 4.Joint Carnegie Mellon University, University of Pittsburgh Program in Computational BiologyPittsburghUSA
  5. 5.Department of Computer ScienceIowa State UniversityAmesUSA
  6. 6.Center for Integrated Animal GenomicsIowa State UniversityAmesUSA

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