IMAD: flexible annotation of microarray sequences

Prickett Dennis, Watson, Michael Watson

Description

Accurate and current functional annotation of microarray probes is essential for the analysis and interpretation of the biological processes involved. As gene structures and functional annotation are updated in genome databases, the annotation attached to microarray probes must be updated so that scientists have access to the latest information with which to analyse their data. Results We have designed a pipeline and database for the annotation of microarray probes using publically available databases. The pipeline is based on NCBI BLAST, Perl and MySQL. The pipeline was used to annotate a subset of 791 differentially expressed ArkGenomics chicken probes from an experiment involving chickens infected with the protozoan parasite Eimeria . Using our pipeline, 770 of the probes were assigned at least one entry in either the Ensembl, UniGene or the DFCI gene indices databases. Conclusion The pipeline described here provides a simple and robust way of maintaining up-to-date and accurate annotation for microarray probes. The pipeline is designed in such a way as to be flexible and easy to update with new information.

Informations

• Publié par: biomed
• Publié le: 01 janvier 2009
• Nombre de lectures: 299
• Langue: English

Extrait

BMC Proceedings

Research IMAD: flexible annotation of microarray sequences Dennis Prickett* and Michael Watson

Address: Bioinformatics Group, Institute for Animal Health (IAH), Compton, Newbury, RG20 7NN, UK Email: Dennis Prickett*  [e-mail]; Michael Watson  [e-mail] * Corresponding author

fromEADGENE and SABRE Post-analyses Workshop Lelystad, The Netherlands. 12–14 November 2008

Published: 16 July 2009 BMC Proceedings2009,3(Suppl 4):S2

doi:10.1186/1753-6561-3-S4-S2

BioMedCentral

Open Access

<supplement><title><p>EADGENEandSABREPost-analysesWorkshop</p></title><editor>Dirk-JandeKoning</editor><sponsor><note>ThepubilcationoftheseproceedingswassupportedbytheEC-fundedNetworkofExcellenceEADGENE(ECcontractnumberFOOD-CT-2004-506416).</note></sponsor><note>Proceedings</note><url>http/:/www.biomedcentral.com/content/pd/f1753-6561-3-S4-info.pdf</url></supplement> This article is available from: http://www.biomedcentral.com/1753-6561/3/S4/S2 © 2009 Prickett and Watson; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract Background:Accurate and current functional annotation of microarray probes is essential for the analysis and interpretation of the biological processes involved. As gene structures and functional annotation are updated in genome databases, the annotation attached to microarray probes must be updated so that scientists have access to the latest information with which to analyse their data. Results:We have designed a pipeline and database for the annotation of microarray probes using publically available databases. The pipeline is based on NCBI BLAST, Perl and MySQL. The pipeline was used to annotate a subset of 791 differentially expressed ArkGenomics chicken probes from an experiment involving chickens infected with the protozoan parasiteEimeria. Using our pipeline, 770 of the probes were assigned at least one entry in either the Ensembl, UniGene or the DFCI gene indices databases. Conclusion:The pipeline described here provides a simple and robust way of maintaining up-to- date and accurate annotation for microarray probes. The pipeline is designed in such a way as to be flexible and easy to update with new information.

Background The use of microarrays plays an important role in biomed ical research, producing large quantities of data on genes that are differentially expressed under various conditions. Although annotation provided with the microarray may be current at the time of manufacture, regular reannota tion of the microarray is essential to keep the annotation current. Additionally, probes may be designed from anno tation based on incomplete genomes and incorrect or incomplete annotation. This may result in an incomplete coverage of the genome, nonspecific probes, incorrect annotation, and orphan probes.

ProbeLynx [1] is a software system that has been pub lished to accomplish the task of linking microarray sequences to annotation data. However, ProbeLynx uses certain tables directly from the Ensembl database and is therefore sensitive to schema changes. At the time of writ ing, ProbeLynx uses Ensembl version 47 (we are currently on version 52). Our objective is to design a flexible, upto date annotation pipeline that can be used to regularly update the annotation of microarray probes using pub licly accessible databases which provide coverage of the genome. This paper is part of a workshop to compare dif

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