rePROBE

rePROBE revises probe assignment and updates probe-set annotation in microarrays to integrate current genomic and transcriptomic information for more accurate gene expression analysis.

Key Features:

• Revised Probe Assignment: Reassigns probes across commercial and customized microarray platforms using up-to-date species-specific genomic and transcriptomic databases such as RefSeq, Ensembl, and non-redundant nucleotide sequences.
• Updated Probe-Set Annotation: Annotates probe sets with current information to link probe sets to unique genes and improve interpretation of gene-level measurements.
• Comprehensive Database Integration: Integrates public and custom databases and supports microarray platforms for livestock species (chicken, pig, cattle) as well as human and mouse.

Scientific Applications:

• Gene Expression Analysis: Enables more accurate cross-species gene expression profiling by providing revised probe assignments and updated annotations.
• Quantitative Trait Locus (QTL) and eQTL Studies: Supports identification of single nucleotide polymorphisms (SNPs) within targeted genomic regions to facilitate eQTL and quantitative/functional trait analyses.

Methodology:

Integrates transcriptomic information from RefSeq, Ensembl and non-redundant nucleotide sequences to reassess probe assignments and probe-set annotations across microarray platforms; applied to ChiGene-1_0-st (chicken), PorGene-1_1-st (pig), BovGene-1_0-st (cattle), HuGene-1_0-st (human) and HT_MG-430_PM (mouse), resulting in reassignment of probes to probe sets representing thousands of unique genes.