A verification protocol for the probe sequences of Affymetrix genome arrays reveals high probe accuracy for studies in mouse,human and rat |
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| Authors: | Rudi Alberts Peter Terpstra Menno Hardonk Leonid V Bystrykh Gerald de Haan Rainer Breitling Jan-Peter Nap Ritsert C Jansen |
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| Institution: | (1) Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9751 NN Haren, kreklaan, The Netherlands;(2) Groningen Bioinformatics Centre, University Medical Centre Groningen, University of Groningen, 9713 AV Groningen, The Netherlands;(3) Department of Cell Biology, section Stem Cell Biology, University Medical Centre Groningen, University of Groningen, 9713 AV Groningen, The Netherlands;(4) Bioinformatics Expertise Center, Institute for Life Science & Technology, Hanze University Groningen, 9747 AS Groningen, The Netherlands |
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| Abstract: | Background The Affymetrix GeneChip technology uses multiple probes per gene to measure its expression level. Individual probe signals
can vary widely, which hampers proper interpretation. This variation can be caused by probes that do not properly match their
target gene or that match multiple genes. To determine the accuracy of Affymetrix arrays, we developed an extensive verification
protocol, for mouse arrays incorporating the NCBI RefSeq, NCBI UniGene Unique, NIA Mouse Gene Index, and UCSC mouse genome
databases. |
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