Annotation and <i>in silico</i> localization of the Affymetrix GeneChip Porcine Genome Array

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.

Transcriptional response of skeletal muscle to a low-protein gestation diet in porcine offspring accumulates in growth- and cell cycle-regulating pathways

“…Further filtering based on the variability of expression of probe sets revealed 14,058 probe sets for further analysis. These probe sets represent 10,028 genes according to the recent annotation (27).…”

“…Analysis of the pathways involved was carried out using Ingenuity Pathway Analysis (IPA) (15). The up-to-date annotation of Affymetrix probe sets to EnsEMBL Sscofa 9 (20,439 of 23,935 annotated probe sets) was used (27). All the microarray data are MIAME compliant, and the raw data have been deposited in an MIAME compliant database, the National Center for Biotechnology Information Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/ geo) (accession numbers: GSE33737 and GSE33739).…”

Gene expression analysis of mammary tissue during fetal bud formation and growth in two pig breeds – indications of prenatal initiation of postnatal phenotypic differences

“…Corresponding q-values were calculated according to algorithms established by Storey [53] using QVALUE. Based on BLAST comparison of the Affymetrix porcine target sequences with the porcine genome sequence (Ensembl_Sscrofa_9), 20,689 of the 24,123 probe sets on the Affymetrix Porcine GeneChip were annotated [54]. This source of annotation was used in this study for Ingenuity Pathways Analysis (IPA) (Ingenuity Systems, http://www.ingenuity.com).…”

Distinctive Genes Determine Different Intramuscular Fat and Muscle Fiber Ratios of the longissimus dorsi Muscles in Jinhua and Landrace Pigs

“…Based on a home-made porcine cDNA microarray carrying 5,500 cDNA clones, Bai et al identified 115 differentially expressed genes between the psoas (red muscle) and the longissimus dorsi (white muscle) of a 22-week-old Berkshire pig [17]. Over the past decade, a tremendous amount of porcine transcriptomics data has been obtained using the pig cDNA microarray [18]–[20], while the Affymetrix porcine genome array showed particularly superior performance for swine transcriptomics [21], [22]. However, reports on the comparison of global gene expression patterns in the skeletal muscles of different pig breeds at different developmental stages are lacking.…”