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

Research output: Contribution to journalArticle

23 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)768-777
Number of pages10
JournalMammalian Genome
Volume20
Issue number11-12
DOIs
StatePublished - Nov 23 2009

Fingerprint

Swine
Databases
Consensus Sequence
Sequence Alignment
Expressed Sequence Tags
Livestock
Single Nucleotide Polymorphism
Research Personnel
Gene Expression
Genes

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

Couture, O., Callenberg, K., Koul, N., Pandit, S., Younes, R., Hu, Z. L., ... Tuggle, C. (2009). ANEXdb: An integrated animal ANnotation and microarray EXpression database. Mammalian Genome, 20(11-12), 768-777. https://doi.org/10.1007/s00335-009-9234-1
Couture, Oliver ; Callenberg, Keith ; Koul, Neeraj ; Pandit, Sushain ; Younes, Remy ; Hu, Zhi Liang ; Dekkers, Jack ; Reecy, James ; Honavar, Vasant ; Tuggle, Christopher. / ANEXdb : An integrated animal ANnotation and microarray EXpression database. In: Mammalian Genome. 2009 ; Vol. 20, No. 11-12. pp. 768-777.
@article{b12748ce4cd64917bd629e6178558c5b,
title = "ANEXdb: An integrated animal ANnotation and microarray EXpression database",
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.",
author = "Oliver Couture and Keith Callenberg and Neeraj Koul and Sushain Pandit and Remy Younes and Hu, {Zhi Liang} and Jack Dekkers and James Reecy and Vasant Honavar and Christopher Tuggle",
year = "2009",
month = "11",
day = "23",
doi = "10.1007/s00335-009-9234-1",
language = "English (US)",
volume = "20",
pages = "768--777",
journal = "Mammalian Genome",
issn = "0938-8990",
publisher = "Springer New York",
number = "11-12",

}

Couture, O, Callenberg, K, Koul, N, Pandit, S, Younes, R, Hu, ZL, Dekkers, J, Reecy, J, Honavar, V & Tuggle, C 2009, 'ANEXdb: An integrated animal ANnotation and microarray EXpression database', Mammalian Genome, vol. 20, no. 11-12, pp. 768-777. https://doi.org/10.1007/s00335-009-9234-1

ANEXdb : An integrated animal ANnotation and microarray EXpression database. / Couture, Oliver; Callenberg, Keith; Koul, Neeraj; Pandit, Sushain; Younes, Remy; Hu, Zhi Liang; Dekkers, Jack; Reecy, James; Honavar, Vasant; Tuggle, Christopher.

In: Mammalian Genome, Vol. 20, No. 11-12, 23.11.2009, p. 768-777.

Research output: Contribution to journalArticle

TY - JOUR

T1 - ANEXdb

T2 - An integrated animal ANnotation and microarray EXpression database

AU - Couture, Oliver

AU - Callenberg, Keith

AU - Koul, Neeraj

AU - Pandit, Sushain

AU - Younes, Remy

AU - Hu, Zhi Liang

AU - Dekkers, Jack

AU - Reecy, James

AU - Honavar, Vasant

AU - Tuggle, Christopher

PY - 2009/11/23

Y1 - 2009/11/23

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=73549089261&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=73549089261&partnerID=8YFLogxK

U2 - 10.1007/s00335-009-9234-1

DO - 10.1007/s00335-009-9234-1

M3 - Article

C2 - 19936830

AN - SCOPUS:73549089261

VL - 20

SP - 768

EP - 777

JO - Mammalian Genome

JF - Mammalian Genome

SN - 0938-8990

IS - 11-12

ER -

Couture O, Callenberg K, Koul N, Pandit S, Younes R, Hu ZL et al. ANEXdb: An integrated animal ANnotation and microarray EXpression database. Mammalian Genome. 2009 Nov 23;20(11-12):768-777. https://doi.org/10.1007/s00335-009-9234-1