AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets Export

@article{Liu2007b, abstract = {Motivation: Affymetrix microarrays are widely used to measure global expression of mRNA transcripts. That technology is based on the concept of a probe set. Individual probes within a probe set were originally designated by Affymetrix to hybridize with the same unique mRNA transcript. Because of increasing accuracy in knowledge of genomic sequences, however, a substantial number of the manufacturer's original probe groupings and mappings are now known to be inaccurate and must be corrected. Otherwise, analysis and interpretation of an Affymetrix microarray experiment will be in error. Results: AffyProbeMiner is a computationally efficient platform-independent tool that uses all RefSeq mature RNA protein coding transcripts and validated complete coding sequences in GenBank to (1) regroup the individual probes into consistent probe sets and (2) remap the probe sets to the correct sets of mRNA transcripts. The individual probes are grouped into probe sets that are transcript-consistent' in that they hybridize to the same mRNA transcript (or transcripts) and, therefore, measure the same entity (or entities). About 65.6 \% of the probe sets on the HG-U133A chip were affected by the remapping. Pre-computed regrouped and remapped probe sets for many Affymetrix microarrays are made freely available at the AffyProbeMiner web site. Alternatively, we provide a web service that enables the user to perform the remapping for any type of short-oligo commercial or custom array that has an Affymetrix-format Chip Definition File (CDF). Important features that differentiate AffyProbeMiner from other approaches are flexibility in the handling of splice variants, computational efficiency, extensibility, customizability and user-friendliness of the interface. Availability: The web interface and software (GPL open source license), are publicly-accessible at http://discover.nci.nih.gov/affyprobeminer. Contact: hl224@georgetown.edu or barry@discover.nci.nih.gov 10.1093/bioinformatics/btm360}, address = {Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.}, author = {Liu, Hongfang and Zeeberg, Barry R. R. and Gang, Qu and Gunes and Ferrucci, Alessandro and Kahn, Ari and Ryan, Michael C. C. and Nuhanovic, Antej and Munson, Peter J. J. and Reinhold, William C. C. and Kane, David W. W. and Weinstein, John N. N.}, booktitle = {Bioinformatics}, citeulike-article-id = {1573312}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btm360}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/18/2385}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/17660211}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=17660211}, day = {15}, doi = {10.1093/bioinformatics/btm360}, issn = {1460-2059}, journal = {Bioinformatics (Oxford, England)}, keywords = {affymetrix, bio-tools, correction, methods}, month = {September}, number = {18}, pages = {2385--2390}, posted-at = {2007-09-17 14:18:46}, priority = {2}, title = {AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets}, url = {http://dx.doi.org/10.1093/bioinformatics/btm360}, volume = {23}, year = {2007} }

TY - JOUR ID - Liu2007b L3 - citeulike-article-id:1573312 N2 - Motivation: Affymetrix microarrays are widely used to measure global expression of mRNA transcripts. That technology is based on the concept of a probe set. Individual probes within a probe set were originally designated by Affymetrix to hybridize with the same unique mRNA transcript. Because of increasing accuracy in knowledge of genomic sequences, however, a substantial number of the manufacturer's original probe groupings and mappings are now known to be inaccurate and must be corrected. Otherwise, analysis and interpretation of an Affymetrix microarray experiment will be in error. Results: AffyProbeMiner is a computationally efficient platform-independent tool that uses all RefSeq mature RNA protein coding transcripts and validated complete coding sequences in GenBank to (1) regroup the individual probes into consistent probe sets and (2) remap the probe sets to the correct sets of mRNA transcripts. The individual probes are grouped into probe sets that are transcript-consistent' in that they hybridize to the same mRNA transcript (or transcripts) and, therefore, measure the same entity (or entities). About 65.6 % of the probe sets on the HG-U133A chip were affected by the remapping. Pre-computed regrouped and remapped probe sets for many Affymetrix microarrays are made freely available at the AffyProbeMiner web site. Alternatively, we provide a web service that enables the user to perform the remapping for any type of short-oligo commercial or custom array that has an Affymetrix-format Chip Definition File (CDF). Important features that differentiate AffyProbeMiner from other approaches are flexibility in the handling of splice variants, computational efficiency, extensibility, customizability and user-friendliness of the interface. Availability: The web interface and software (GPL open source license), are publicly-accessible at http://discover.nci.nih.gov/affyprobeminer. Contact: hl224@georgetown.edu or barry@discover.nci.nih.gov 10.1093/bioinformatics/btm360 IS - 18 JF - Bioinformatics (Oxford, England) SN - 1460-2059 AD - Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA. EP - 2390 TI - AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets VL - 23 T2 - Bioinformatics SP - 2385 KW - affymetrix KW - bio-tools KW - correction KW - methods AU - Liu, Hongfang AU - Zeeberg, Barry AU - Gang, Qu AU - Gunes AU - Ferrucci, Alessandro AU - Kahn, Ari AU - Ryan, Michael AU - Nuhanovic, Antej AU - Munson, Peter AU - Reinhold, William AU - Kane, David AU - Weinstein, John PY - 2007/09/15/ UR - http://dx.doi.org/10.1093/bioinformatics/btm360 ER -