Characterization of mismatch and high-signal intensity probes associated with Affymetrix genechips
文献类型：期刊论文
| 作者 | Wang, Yonghong; Miao, Ze-Hong; Pommier, Yves; Kawasaki, Ernest S.; Player, Audrey |
| 刊名 | BIOINFORMATICS
 |
| 出版日期 | 2007-08-15 |
| 卷号 | 23期号:16页码:2088-2095 |
| ISSN号 | 1367-4803 |
| DOI | 10.1093/bioinformatics/btm306 |
| 文献子类 | Article |
| 英文摘要 | Motivation: For Affymetrix microarray platforms, gene expression is determined by computing the difference in signal intensities between perfect match ( PM) and mismatch ( MM) probesets. Although the use of PM is not controversial, MM probesets have been associated with variance and ultimately inaccurate gene expression calls. A principal focus of this study was to investigate the nature of the MM signal intensities and demonstrate its contribution to the experimental results. Results: While most MM intensities were likely associated with random noise, a subset of similar to 20% ( 99 485) of the MM probes displayed relatively high signal intensities to the corresponding PM probes (MM > PM) in a non-random fashion; 13 440 of these probes demonstrated exceptionally high 'outlier' intensities. About 15 938 PM probes also demonstrated exceptionally high outlier intensities consistently across all hybridizations. About 92% of the MM > PM probes had either a dThymidine (dT) or a dCytidine (dC) at the 13th position of the probe sequence. MM and PM probes displaying extremely high outlier intensities contained high dC rich nucleotides, and low dA contents at other nucleotides positions along the 25mer probe sequence. Differentially expressed genes generated using Genechip Operating System (GCOS) or modified PM-only methods were also examined. Of those candidate genes identified in the PM-only method, 157 of them were designated by GCOS as absent across all datasets and many others contained probes with MM > PM signal intensities. Our data suggests that MM intensity from PM signal can be a major source of error analysis, leading to fewer potentially biologically important candidate genes. Contact: wangyong@mail.nih.gov Supplementary information: Supplementary data are available at Bioinformatics online. |
| WOS关键词 | MICROARRAY ; ARRAY ; HYBRIDIZATION ; NORMALIZATION |
| 资助项目 | NCI NIH HHS[N01-CO-12400] |
| WOS研究方向 | Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics |
| 语种 | 英语 |
| WOS记录号 | WOS:000249818300008 |
| 出版者 | OXFORD UNIV PRESS |
| 源URL | [http://119.78.100.183/handle/2S10ELR8/273175]  |
| 专题 | 中国科学院上海药物研究所 |
| 通讯作者 | Wang, Yonghong |
| 作者单位 | 1.Ctr Canc Res, NCI, Mol Pharmacol Lab, Bethesda, MD 20892 USA 2.NCI, NIH, Microarray Core Facil, Bethesda, MD 20892 USA 3.SAIC Frederick Inc, NCI, Ft Detrick, MD 21702 USA |
| 推荐引用方式 GB/T 7714 | Wang, Yonghong,Miao, Ze-Hong,Pommier, Yves,et al. Characterization of mismatch and high-signal intensity probes associated with Affymetrix genechips[J]. BIOINFORMATICS,2007,23(16):2088-2095. |
| APA | Wang, Yonghong,Miao, Ze-Hong,Pommier, Yves,Kawasaki, Ernest S.,&Player, Audrey.(2007).Characterization of mismatch and high-signal intensity probes associated with Affymetrix genechips.BIOINFORMATICS,23(16),2088-2095. |
| MLA | Wang, Yonghong,et al."Characterization of mismatch and high-signal intensity probes associated with Affymetrix genechips".BIOINFORMATICS 23.16(2007):2088-2095. |
入库方式： OAI收割
来源：上海药物研究所
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