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rePROBE:Workflow for Revised Probe Assignment and Updated Probe-set Annotation in Microarrays

Genomics, Proteomics & Bioinformatics 2021年第6期19卷 1043-1049页

作者： Frieder Hadlich Henry Reyer Michael Oster Nares Trakooljul Eduard Muráni siriluck ponsuksili Klaus Wimmers Research Institute for Farm Animal Biology(FBN) Institute of Genome BiologyD-18196 DummerstorfGermany Faculty of Agricultural and Environmental Sciences University of RostockD-18059 RostockGermany

Commercial and customized microarrays are valuable tools for the analysis of holistic expression patterns,but require the integration of the latest genomic *** study provides a comprehensive workflow implemented in an R package(rePROBE)to assign the entire probes and to annotate the probe sets based on up-to-date genomic and transcriptomic *** rePROBE package can be applied to available gene expression microarray platforms and addresses both public and custom *** revised probe assignment and updated probe-set annotation are applied to commercial microarrays available for different livestock species,i.e.,chicken(Gallus gallus;ChiGene-1_0-st:443,579 probes and 18,530 probe sets),pig(Sus scrofa;PorGene-1_1-st:592,005 probes and 25,779 probe sets),and cattle(Bos Taurus;BovGene-1_0-st:530,717 probes and 24,759 probe sets),as well as available for human(Homo sapiens;HuGene-1_0-st)and mouse(Mus musculus HT_MG-430_PM).Using current species-specific transcriptomic information(RefSeq,Ensembl,and partially non-redundant nucleotide sequences)and genomic information,the applied workflow reveals 297,574 probes(15,689 probe sets)for chicken,384,715 probes(21,673 probe sets)for pig,363,077 probes(21,238 probe sets)for cattle,481,168 probes(23,495 probe sets)for human,and 324,942 probes(32,494 probe sets)for *** are representative of 12,641,15,758,18,046,20,167,and 16,335 unique genes that are both annotated and positioned for chicken,pig,cattle,human,and mouse,***,the workflow collects information on the number of single nucleotide polymorphisms(SNPs)within respective targeted genomic regions and thus provides a detailed basis for comprehensive analyses such as expression quantitative trait locus(eQTL)studies to identify quantitative and functional *** rePROBE R package is freely available at https://***/friederhadlich/rePROBE.

关键词： Mapping Microarray Probe assignment Probe-set annotation Genomic database

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Applicability of a Variance Components Method for QTL Mapping in Comparison with Haley-Knott Regressions

Applicability of a Variance Components Method for QTL Mappin...

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2003北京国际养猪研讨会暨展览会

作者： Heinz-Josef Schreinemachers Ernst Tholen Klaus Wimmers siriluck ponsuksili Karl chellander Institute of Animal Breeding and Geneics Uiversity of BonnEndenicher Allee 15D-53115 BonnGermany Institute of Animal Breeding and Geneics Uiversity of BonnEndenicher Allee 15D-53115 BonnGermany Institute of Animal Breeding and Geneics Uiversity of BonnEndenicher Allee 15D-53115 BonnGermany Institute of Animal Breeding and Geneics Uiversity of BonnEndenicher Allee 15D-53115 BonnGermany Institute of Animal Breeding and Geneics Uiversity of BonnEndenicher Allee 15D-53115 BonnGermany

＜正＞ Introduction and objective In modern pig-breeding organizations, marker data from nucleus lines recorded in several generationsare available. Standard methods like Haly-Knott regression [3] are restricted to specific pedigree designsand therefore they are not fully applicable to thes kind of data. In general, vedance components methods（VC） are more flexible in handling of several traits with different underlying distributions and a complexpedigree structure. Applying these methods in QTL-mapping, the estimation of the proportion of variancecontributed by a QTL at a specific locus is feasible. In order to separate additive genetic and QTL-variance,

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