ProbeLynx: A tool for updating the association of microarray probes to genes

Fiona M. Roche, Karsten Hokamp, Michael Acab, Lorne A. Babiuk, Robert Hancock, Fiona S.L. Brinkman

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

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 servicewhichusescurrentgenomicsequenceinformation 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.

LanguageEnglish
JournalNucleic acids research
Volume32
Issue numberWEB SERVER ISS.
DOIs
Publication statusPublished - 1 Jul 2004

ASJC Scopus subject areas

  • Genetics

Cite this

Roche, F. M., Hokamp, K., Acab, M., Babiuk, L. A., Hancock, R., & Brinkman, F. S. L. (2004). ProbeLynx: A tool for updating the association of microarray probes to genes. Nucleic acids research, 32(WEB SERVER ISS.). https://doi.org/10.1093/nar/gkh452
Roche, Fiona M. ; Hokamp, Karsten ; Acab, Michael ; Babiuk, Lorne A. ; Hancock, Robert ; Brinkman, Fiona S.L. / ProbeLynx : A tool for updating the association of microarray probes to genes. In: Nucleic acids research. 2004 ; Vol. 32, No. WEB SERVER ISS.
@article{20680096004c4960a62ecaeadc98d5e0,
title = "ProbeLynx: A tool for updating the association of microarray probes to genes",
abstract = "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 servicewhichusescurrentgenomicsequenceinformation 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.",
author = "Roche, {Fiona M.} and Karsten Hokamp and Michael Acab and Babiuk, {Lorne A.} and Robert Hancock and Brinkman, {Fiona S.L.}",
year = "2004",
month = "7",
day = "1",
doi = "10.1093/nar/gkh452",
language = "English",
volume = "32",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "WEB SERVER ISS.",

}

Roche, FM, Hokamp, K, Acab, M, Babiuk, LA, Hancock, R & Brinkman, FSL 2004, 'ProbeLynx: A tool for updating the association of microarray probes to genes', Nucleic acids research, vol. 32, no. WEB SERVER ISS.. https://doi.org/10.1093/nar/gkh452

ProbeLynx : A tool for updating the association of microarray probes to genes. / Roche, Fiona M.; Hokamp, Karsten; Acab, Michael; Babiuk, Lorne A.; Hancock, Robert; Brinkman, Fiona S.L.

In: Nucleic acids research, Vol. 32, No. WEB SERVER ISS., 01.07.2004.

Research output: Contribution to journalArticle

TY - JOUR

T1 - ProbeLynx

T2 - Nucleic Acids Research

AU - Roche, Fiona M.

AU - Hokamp, Karsten

AU - Acab, Michael

AU - Babiuk, Lorne A.

AU - Hancock, Robert

AU - Brinkman, Fiona S.L.

PY - 2004/7/1

Y1 - 2004/7/1

N2 - 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 servicewhichusescurrentgenomicsequenceinformation 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.

AB - 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 servicewhichusescurrentgenomicsequenceinformation 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.

UR - http://www.scopus.com/inward/record.url?scp=3242882897&partnerID=8YFLogxK

U2 - 10.1093/nar/gkh452

DO - 10.1093/nar/gkh452

M3 - Article

VL - 32

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - WEB SERVER ISS.

ER -