Document Detail

Significance analysis of microarrays applied to the ionizing radiation response.
MedLine Citation:
PMID:  11309499     Owner:  NLM     Status:  MEDLINE    
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.
V G Tusher; R Tibshirani; G Chu
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, P.H.S.     Date:  2001-04-17
Journal Detail:
Title:  Proceedings of the National Academy of Sciences of the United States of America     Volume:  98     ISSN:  0027-8424     ISO Abbreviation:  Proc. Natl. Acad. Sci. U.S.A.     Publication Date:  2001 Apr 
Date Detail:
Created Date:  2001-04-26     Completed Date:  2001-05-21     Revised Date:  2009-11-18    
Medline Journal Info:
Nlm Unique ID:  7505876     Medline TA:  Proc Natl Acad Sci U S A     Country:  United States    
Other Details:
Languages:  eng     Pagination:  5116-21     Citation Subset:  IM    
Departments of Medicine and Biochemistry, Stanford University, 269 Campus Drive, Center for Clinical Sciences Research 1115, Stanford, CA 94305-5151, USA.
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MeSH Terms
Apoptosis / genetics,  radiation effects
Cell Cycle / genetics,  radiation effects
DNA Damage / genetics,  radiation effects
DNA Repair / genetics
Down-Regulation / radiation effects
Gene Expression Profiling*
Gene Expression Regulation / radiation effects*
Oligonucleotide Array Sequence Analysis*
RNA, Messenger / genetics,  metabolism
Radiation, Ionizing
Reproducibility of Results
Statistics as Topic
Tumor Cells, Cultured
Up-Regulation / radiation effects
Grant Support
Reg. No./Substance:
0/RNA, Messenger
Erratum In:
Proc Natl Acad Sci U S A 2001 Aug 28;98(18):10515

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