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

Vered Chalifa-Caspi; Itai Yanai; Ron Ophir; Naomi Rosen; Michael Shmoish; Hila Benjamin-Rodrig; Maxim Shklar; Tsippi Iny Stein; Orit Shmueli; Marilyn Safran; Doron Lancet

doi:10.1093/bioinformatics/bth081

PubMed · 14962929

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

Vered Chalifa-Caspi·Itai Yanai·Ron Ophir·Naomi Rosen·Michael Shmoish·Hila Benjamin-Rodrig·Maxim Shklar·Tsippi Iny Stein·Orit Shmueli·Marilyn Safran·Doron Lancet

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Abstract

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. AVAILABILITY: http://genecards.weizmann.ac.il/geneannot/ SUPPLEMENTARY INFORMATION: Program description and statistics http://genecards.weizmann.ac.il/geneannot/DOC/index.html

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Algorithms Chromosome Mapping Documentation Oligonucleotide Array Sequence Analysis Sequence Alignment Sequence Analysis, DNA Software Comparative Study Evaluation Study Journal Article Research Support, Non-U.S. Gov't

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Vered Chalifa-Caspi, Itai Yanai, Ron Ophir, Naomi Rosen, Michael Shmoish, Hila Benjamin-Rodrig, Maxim Shklar, Tsippi Iny Stein, Orit Shmueli, Marilyn Safran, Doron Lancet. 2004-02-12. GeneAnnot: comprehensive two-way linking between oligonucleotide array probesets and GeneCards genes.. https://doi.org/10.1093/bioinformatics%2Fbth081

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