Journal ArticleDOI
Microarray data normalization and transformation
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TLDR
This review focuses on the much more mundane but indispensable tasks of 'normalizing' data from individual hybridizations to make meaningful comparisons of expression levels, and of 'transforming' them to select genes for further analysis and data mining.Abstract:
Underlying every microarray experiment is an experimental question that one would like to address. Finding a useful and satisfactory answer relies on careful experimental design and the use of a variety of data-mining tools to explore the relationships between genes or reveal patterns of expression. While other sections of this issue deal with these lofty issues, this review focuses on the much more mundane but indispensable tasks of 'normalizing' data from individual hybridizations to make meaningful comparisons of expression levels, and of 'transforming' them to select genes for further analysis and data mining.read more
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Cross-species global and subset gene expression profiling identifies genes involved in prostate cancer response to selenium
Michael J. Schlicht,Michael J. Schlicht,Brian Matysiak,Tracy Brodzeller,Xinyu Wen,Hang Liu,Guohui Zhou,Guohui Zhou,Rajiv Dhir,Martin J. Hessner,Peter J. Tonellato,Mark A. Suckow,Morris Pollard,Milton W. Datta,Milton W. Datta +14 more
TL;DR: A comparative genomics based method to leverage data from animal models to prioritize genes for validation, and provides a method for identifying testable functional pathways for the action of Selenium's chemopreventive properties in prostate cancer.
Journal ArticleDOI
Genetic study of alcoholism and novel gene expression in the alcoholic brain.
TL;DR: The current information on the genetic basis of alcoholism and the induction and characterization of alcohol‐responsive genes is discussed and a wide range of functions in the brain are indicated.
Journal ArticleDOI
Distinct gene expression profiles in peripheral blood mononuclear cells from patients infected with vaccinia virus, yellow fever 17D virus, or upper respiratory infections.
Christina A. Scherer,Charles L. Magness,Kathryn V. Steiger,Nicholas D. Poitinger,Christine M. Caputo,Douglas G. Miner,Patricia L. Winokur,Donna Klinzman,Janice McKee,Christine Pilar,Patricia A. Ward,Martha H. Gillham,N. Jean Haulman,Jack T. Stapleton,Shawn P. Iadonato +14 more
TL;DR: Gene expression in human peripheral blood mononuclear cells was systematically evaluated following smallpox and yellow fever vaccination, and naturally occurring upper respiratory infection, to suggest that specific host gene expression signatures may be identified that distinguish one or a small number of virus agents.
Journal ArticleDOI
Imatinib Treatment Causes Substantial Transcriptional Changes in Adult Schistosoma mansoni In Vitro Exhibiting Pleiotropic Effects
Christin Buro,Svenja Beckmann,Katia C. Oliveira,Colette Dissous,Katia Cailliau,Richard J. Marhöfer,Paul M. Selzer,Sergio Verjovski-Almeida,Christoph G. Grevelding +8 more
TL;DR: The data affirm broad negative effects of Imatinib on worm physiology substantiating the role of PKs as interesting targets and first evidence for an association of TGFβ and Abl kinase signaling.
Journal ArticleDOI
Systematic gene expression profiling of mouse model series reveals coexpressed genes.
Marion Horsch,Sandra Schädler,Valerie Gailus-Durner,Helmut Fuchs,Helmut E. Meyer,Martin Hrabé de Angelis,Johannes Beckers +6 more
TL;DR: The efficiency of systematic genome‐wide expression profiling for the detection of molecular phenotypes in organs of a mammalian model organism is demonstrated and the recurring regulation of particular genes and groups of coexpressed genes in apparently unrelated MMLs are identified.
References
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Journal ArticleDOI
Cluster analysis and display of genome-wide expression patterns
TL;DR: A system of cluster analysis for genome-wide expression data from DNA microarray hybridization is described that uses standard statistical algorithms to arrange genes according to similarity in pattern of gene expression, finding in the budding yeast Saccharomyces cerevisiae that clustering gene expression data groups together efficiently genes of known similar function.
Book
Data Reduction and Error Analysis for the Physical Sciences
TL;DR: In this paper, Monte Carlo techniques are used to fit dependent and independent variables least squares fit to a polynomial least-squares fit to an arbitrary function fitting composite peaks direct application of the maximum likelihood.
Journal ArticleDOI
Data Reduction and Error Analysis for the Physical Sciences.
TL;DR: Numerical methods matrices graphs and tables histograms and graphs computer routines in Pascal and Monte Carlo techniques dependent and independent variables least-squares fit to a polynomial least-square fit to an arbitrary function fitting composite peaks direct application of the maximum likelihood.
Journal ArticleDOI
Robust Locally Weighted Regression and Smoothing Scatterplots
TL;DR: Robust locally weighted regression as discussed by the authors is a method for smoothing a scatterplot, in which the fitted value at z k is the value of a polynomial fit to the data using weighted least squares, where the weight for (x i, y i ) is large if x i is close to x k and small if it is not.
Book
Regression Analysis by Example
Samprit Chatterjee,B. Price +1 more
TL;DR: Simple linear regression Multiple linear regression Regression Diagnostics: Detection of Model Violations Qualitative Variables as Predictors Transformation of Variables Weighted Least Squares The Problem of Correlated Errors Analysis of Collinear Data Biased Estimation of Regression Coefficients Variable Selection Procedures Logistic Regression Appendix References as discussed by the authors