Mar 11, 2020

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

bioRxiv
Frieder HadlichKlaus Wimmers

Abstract

Commercial and customized microarrays are valuable tools for the analysis of holistic expression patterns, but require the integration of the latest genomic information. This 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 information. The rePROBE R package is freely available at https://github.com/friederhadlich/rePROBE. It can be applied to available gene expression microarray platforms and addresses both public and custom databases. The revised probe assignment and updated probe-set annotation were applied to commercial microarrays available for different livestock species, i.e. ChiGene-1\_0-st (Gallus gallus, 443,579 probes; 18,530 probe sets), PorGene-1\_1-st (Sus scrofa, 592,005; 25,779) and BovGene-1\_0-st (Bos taurus, 530,717; 24,759) as well as human (Homo sapiens, HuGene-1\_0-st) and mouse (Mus musculus, HT\_MG-430\_PM) microarrays. Using current specie-specific transcriptomic information (RefSeq, Ensembl and partially non-redundant nucleotide sequences) and genomic information, the applied workflow revealed 297,574 probes for chickens (pig: 384,715; cattle: 363,077; human: 481,168; m...Continue Reading

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Mentioned in this Paper

Patterns
Transcriptome
Protein Expression
Software Tools
Gallus
Bos taurus
Study
Gene Annotation
Base Sequence
Myasthenia Gravis

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