Adaptable gene‐specific dye bias correction for two‐channel DNA microarrays
Abstract DNA microarray technology is a powerful tool for monitoring gene expression or for finding the location of DNA‐bound proteins. DNA microarrays can suffer from gene‐specific dye bias (GSDB), causing some probes to be affected more by the dye than by the sample. This results in large measurem...
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| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Springer Nature
2009-04-01
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| Series: | Molecular Systems Biology |
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| Online Access: | https://doi.org/10.1038/msb.2009.21 |
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| _version_ | 1850179221317484544 |
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| author | Thanasis Margaritis Philip Lijnzaad Dik van Leenen Diane Bouwmeester Patrick Kemmeren Sander R van Hooff Frank CP Holstege |
| author_facet | Thanasis Margaritis Philip Lijnzaad Dik van Leenen Diane Bouwmeester Patrick Kemmeren Sander R van Hooff Frank CP Holstege |
| author_sort | Thanasis Margaritis |
| collection | DOAJ |
| description | Abstract DNA microarray technology is a powerful tool for monitoring gene expression or for finding the location of DNA‐bound proteins. DNA microarrays can suffer from gene‐specific dye bias (GSDB), causing some probes to be affected more by the dye than by the sample. This results in large measurement errors, which vary considerably for different probes and also across different hybridizations. GSDB is not corrected by conventional normalization and has been difficult to address systematically because of its variance. We show that GSDB is influenced by label incorporation efficiency, explaining the variation of GSDB across different hybridizations. A correction method (Gene‐ And Slide‐Specific Correction, GASSCO) is presented, whereby sequence‐specific corrections are modulated by the overall bias of individual hybridizations. GASSCO outperforms earlier methods and works well on a variety of publically available datasets covering a range of platforms, organisms and applications, including ChIP on chip. A sequence‐based model is also presented, which predicts which probes will suffer most from GSDB, useful for microarray probe design and correction of individual hybridizations. Software implementing the method is publicly available. |
| format | Article |
| id | doaj-art-30df98edcc8f49bcbae66c69663bf88a |
| institution | OA Journals |
| issn | 1744-4292 |
| language | English |
| publishDate | 2009-04-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj-art-30df98edcc8f49bcbae66c69663bf88a2025-08-20T02:18:33ZengSpringer NatureMolecular Systems Biology1744-42922009-04-01511610.1038/msb.2009.21Adaptable gene‐specific dye bias correction for two‐channel DNA microarraysThanasis Margaritis0Philip Lijnzaad1Dik van Leenen2Diane Bouwmeester3Patrick Kemmeren4Sander R van Hooff5Frank CP Holstege6Department of Physiological Chemistry, University Medical Center Utrecht, UniversiteitswegDepartment of Physiological Chemistry, University Medical Center Utrecht, UniversiteitswegDepartment of Physiological Chemistry, University Medical Center Utrecht, UniversiteitswegDepartment of Physiological Chemistry, University Medical Center Utrecht, UniversiteitswegDepartment of Physiological Chemistry, University Medical Center Utrecht, UniversiteitswegDepartment of Physiological Chemistry, University Medical Center Utrecht, UniversiteitswegDepartment of Physiological Chemistry, University Medical Center Utrecht, UniversiteitswegAbstract DNA microarray technology is a powerful tool for monitoring gene expression or for finding the location of DNA‐bound proteins. DNA microarrays can suffer from gene‐specific dye bias (GSDB), causing some probes to be affected more by the dye than by the sample. This results in large measurement errors, which vary considerably for different probes and also across different hybridizations. GSDB is not corrected by conventional normalization and has been difficult to address systematically because of its variance. We show that GSDB is influenced by label incorporation efficiency, explaining the variation of GSDB across different hybridizations. A correction method (Gene‐ And Slide‐Specific Correction, GASSCO) is presented, whereby sequence‐specific corrections are modulated by the overall bias of individual hybridizations. GASSCO outperforms earlier methods and works well on a variety of publically available datasets covering a range of platforms, organisms and applications, including ChIP on chip. A sequence‐based model is also presented, which predicts which probes will suffer most from GSDB, useful for microarray probe design and correction of individual hybridizations. Software implementing the method is publicly available.https://doi.org/10.1038/msb.2009.21DNA microarraysfluorescent dye labellingmRNA expression profilingnormalizationtwo channel |
| spellingShingle | Thanasis Margaritis Philip Lijnzaad Dik van Leenen Diane Bouwmeester Patrick Kemmeren Sander R van Hooff Frank CP Holstege Adaptable gene‐specific dye bias correction for two‐channel DNA microarrays Molecular Systems Biology DNA microarrays fluorescent dye labelling mRNA expression profiling normalization two channel |
| title | Adaptable gene‐specific dye bias correction for two‐channel DNA microarrays |
| title_full | Adaptable gene‐specific dye bias correction for two‐channel DNA microarrays |
| title_fullStr | Adaptable gene‐specific dye bias correction for two‐channel DNA microarrays |
| title_full_unstemmed | Adaptable gene‐specific dye bias correction for two‐channel DNA microarrays |
| title_short | Adaptable gene‐specific dye bias correction for two‐channel DNA microarrays |
| title_sort | adaptable gene specific dye bias correction for two channel dna microarrays |
| topic | DNA microarrays fluorescent dye labelling mRNA expression profiling normalization two channel |
| url | https://doi.org/10.1038/msb.2009.21 |
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