ProbeLynx: a tool for updating the association of microarray probes to genes.
As genome sequence data and gene prediction improve, probes developed for a given microarray experiment should be continuously re-evaluated for their specificity for given genes. ProbeLynx(www.pathogenomics.ca/probelynx) is a new web service which uses current genomic sequence information to re-examine microarray probe specificity and provide annotation updates relevant to determining which gene(s) and transcript(s) are associated with a given probe. Probe sequences (either oligonucleotide- or cDNA-based) are uploaded in FASTA format and the results returned as a tab-delimited flat file for insertion into a spreadsheet application or database management system for further analysis. ProbeLynx has been initially developed to focus on arrays derived from human, mouse, chicken and bovine genomes, but may be expanded to handle other genomic datasets. ProbeLynx offers microarray users the important ability to continuously assess the potential of a probe to cross-hybridize to paralogous genes and the suitability of a given probe to investigate a transcript of interest. By also including the latest gene function annotation information in the output, ProbeLynx provides the critical first step in updating microarray data annotation.
Roche
Fiona M
FM
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.
Hokamp
Karsten
K
Acab
Michael
M
Babiuk
Lorne A
LA
Hancock
Robert E W
RE
Brinkman
Fiona S L
FS
D000818:Animals; D001483:Base Sequence; D002417:Cattle; D002645:Chickens / Q000235:genetics; D015342:DNA Probes / Q000737:chemistry*; D018076:DNA, Complementary / Q000737:chemistry; D030561:Databases, Nucleic Acid; D020869:Gene Expression Profiling; D023281:Genomics; D006801:Humans; D020407:Internet; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis; D015345:Oligonucleotide Probes / Q000737:chemistry; D012333:RNA, Messenger / Q000737:chemistry; D012984:Software
D015342:DNA Probes; D018076:DNA, Complementary; D015345:Oligonucleotide Probes; D012333:RNA, Messenger