GeneAnnot: Comprehensive two-way linking between oligonucleotide array probesets and GeneCards genes

Motivation: High density oligonucleotide arrays are usually annotated in a one-to-one fashion, with each probeset assigned to one gene. However, in reality, subsets of oligonucleotides in a probeset may match sequences within more than one gene, potentially leading to misinterpretations. Moreover, a gene is often represented by more than one probeset, and analyzing probe matches at the mRNA level can help one deduce whether these probesets are derived from the same or different splice variants. Results: The GeneAnnot system comprehensively documents the many-to-many relationship between oligonucleotide array probesets and annotated genes in GeneCards™. It performs pairwise alignments between the probe sequences and gene transcripts, and assigns sensitivity and specificity scores to each probeset/gene pair.