Annotation and &amp;lt;i&amp;gt;in silico&amp;lt;/i&amp;gt; localization of the Affymetrix GeneChip Porcine Genome Array

W Naraballobh,E Murani,S Ponsuksili,S Chomdej,K Wimmers

doi:10.5194/aab-53-230-2010

Abstract

Abstract. Expression microarrays including the Affymetrix GeneChip Porcine Genome Arrays are valuable tools for studying genes and functional networks relevant for the expression of complex traits and the responsiveness of the organism to various treatments. An updated annotation and, for the first time, localization on the porcine physical genome map of »Affymetrix GeneChip Porcine Genome Array probe sets« was made through a workflow of 3 pipelines of comparisions addressing various NCBI (National Center for Biotechnology Information) and EnsEMBL (Ensembl project) databases. »BLAST« (Basic Local Alignment Search Tool) comparisons of Affymetrix probe set consensus sequences with the EnsEMBL Sscrofa 9 cDNA database provided 23 799 probe sets with hits. After annotation 19 730 gene symbols were obtained using the data management system BioMart. Comparison of the Affymetrix probe set consensus sequences with the porcine genome sequence (EnsEMBL Sscrofa 9 LatestGP database) revealed 23 298 probe sets with BLAST hits. In the third pipeline in addition to EnsEMBL Sscrofa 9 cDNA and genomic sequence databases also human, mouse and pig NCBI reference sequence RNA databases were interrogated in an integrated approach where also a threshold of bit score >50 or >90 % identity over >100 bp was applied in order to filter questionable annotations and localizations. Gene symbols and gene names were queried from HGNC (human genome organization (HUGO) gene nomenclature committee), EASE (EASE: the Expression Analysis Systematic Explorer) and Entrez Gene revealing 20 269 annotated probe sets. 20 467 probe sets were in silico mapped addressing various sources: EnsEMBL Sscrofa 9 LatestGP, pre-EnsEMBL Sscrofa 8.52 LatestGP, NCBI pig reference sequence RNA and genomic databases and PigQTLdb (Pig Quantitative Trait Locus [QTL] database). Using the new annotation and localization data in functional genomics studies will facilitate improving the understanding of the control of quantitative traits in pigs.

Highlights

Microarray technologies have enabled the measurement of gene expression levels for thousands of genes in parallel
Results are presented in 26 columns summarizing raw BLAST result (Probe set ID, Blast header result, Blast pair-wise result, High Score, Smallest Sum Probability P(N), N, Query start, Query stop, Subject start, Subject stop, Alignment length, Identity value, Identity value full, % Identity, Chromosome position) and results obtained after querying EnsEMBL Transcript ID with BioMart (SMEDLEY et al 2009) (EnsEMBL Transcript ID, EnsEMBL Gene ID, Gene symbol, Gene name, Chromosome, Gene start, Gene end, Transcript start, Transcript end, EntrezGene ID)
Using three pipelines annotations and localizations of probe sets of the Affymetrix GeneChip Porcine Genome Array were obtained querying EnsEMBL and NCBI databases including non-filtered BLAST results and results meeting thresholds regarding the degree of identity

Summary

Introduction

Microarray technologies have enabled the measurement of gene expression levels for thousands of genes in parallel. Functional genomics provides new opportunities for determining the molecular processes underlying phenotypic variation towards developmental and reproduction traits, growth, immune response and host-pathogen interaction (BAI et al 2003, BAND et al 2002, BERNARD et al 2007, COGBURN et al 2003, MOSER et al 2004, PONSUKSILI et al 2007, 2008a, 2008b, SUCHYTA et al 2003, TUGGLE et al 2007). Several whole genome expression microarrays for pigs are available including consortium arrays like the »Pigoligoarray« (http://www.pigoligoarray.org) or commercial microarrays like the Agilent Porcine Gene Expression Microarray (Agilent Technologies; http://www.chem.agilent.com) and the Affymetrix GeneChip Porcine Genome Array (Affymetrix, http://www.affymetrix.com). The microarray design of Affymetrix GeneChips has been proven to provide highly reproducible expression profiles and is available for many different species (HARTMANN et al 2009).

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