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Significance analysis of microarrays applied to the ionizing radiation response.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Tusher, V. G. Tibshirani, R. Chu, G.
Description	Author Affiliation: Tusher VG ( Departments of Medicine and Biochemistry, Stanford University, 269 Campus Drive, Center for Clinical Sciences Research 1115, Stanford, CA 94305-5151, USA.);
Abstract	Microarrays can measure the expression of thousands of genes to identify changes in expression between different biological states. Methods are needed to determine the significance of these changes while accounting for the enormous number of genes. We describe a method, Significance Analysis of Microarrays (SAM), that assigns a score to each gene on the basis of change in gene expression relative to the standard deviation of repeated measurements. For genes with scores greater than an adjustable threshold, SAM uses permutations of the repeated measurements to estimate the percentage of genes identified by chance, the false discovery rate (FDR). When the transcriptional response of human cells to ionizing radiation was measured by microarrays, SAM identified 34 genes that changed at least 1.5-fold with an estimated FDR of 12%, compared with FDRs of 60 and 84% by using conventional methods of analysis. Of the 34 genes, 19 were involved in cell cycle regulation and 3 in apoptosis. Surprisingly, four nucleotide excision repair genes were induced, suggesting that this repair pathway for UV-damaged DNA might play a previously unrecognized role in repairing DNA damaged by ionizing radiation.
ISSN	00278424
e-ISSN	10916490
Journal	Proceedings of the National Academy of Sciences of the United States of America
Issue Number	9
Volume Number	98
Language	English
Publisher	National Academy of Sciences
Publisher Date	2001-04-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Gene Expression Profiling Gene Expression Regulation Radiation Effects Oligonucleotide Array Sequence Analysis Apoptosis Genetics Cell Cycle DNA Damage DNA Repair Down-Regulation RNA, Messenger Metabolism Radiation, Ionizing Reproducibility Of Results Statistics As Topic Tumor Cells, Cultured Up-Regulation Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S. Multidisciplinary
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

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