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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Journal ArticleDOI
Cytokines and cytokine profiles in human autoimmune diseases and animal models of autoimmunity.
Manfred Kunz,Saleh M. Ibrahim +1 more
TL;DR: Major contributions were made by experiments using DNA microarray technology, which has been used for the analysis of gene expression patterns in chronic inflammatory and autoimmune diseases, among which were rheumatoid arthritis, systemic lupus erythematosus, psoriasis, systemic sclerosis, multiple sclerosis, and type-1 diabetes.
Journal ArticleDOI
Universal Reference RNA as a standard for microarray experiments
Natalia Novoradovskaya,Michael L. Whitfield,Michael L. Whitfield,Lee Scott Basehore,Alexey Novoradovsky,Robert Pesich,Jerry Usary,Mehmet Karaca,Winston K. Wong,Olga Aprelikova,Michael J. Fero,Charles M. Perou,David Botstein,David Botstein,Jeff Braman +14 more
TL;DR: Results of this study demonstrate that large quantities of pooled RNA from individual cell lines are reproducibly prepared and possess diverse gene representation, which provides a standard for reducing variation in microarray experiments and allows more reliable comparison of gene expression data within and between experiments and laboratories.
Journal ArticleDOI
Differential gene expression by Metarhizium anisopliae growing in root exudate and host (Manduca sexta) cuticle or hemolymph reveals mechanisms of physiological adaptation.
TL;DR: There were differences in gene expression between hemolymph and cuticle and these mostly involved perception mechanisms, carbon metabolism, proteolysis, cell surface properties, and synthesis of toxic metabolites, which suggest previously unsuspected stratagems of fungal pathogenicity that can be tested experimentally.
Book ChapterDOI
Oxidative stress responses in yeast
TL;DR: The data reviewed in this article illustrates how much the understanding of the biology of oxidants has advanced, and how much research is still needed to unravel its complexity.
Journal ArticleDOI
Glycoproteomic Analysis of Prostate Cancer Tissues by SWATH Mass Spectrometry Discovers N-acylethanolamine Acid Amidase and Protein Tyrosine Kinase 7 as Signatures for Tumor Aggressiveness
Yansheng Liu,Jing Chen,Atul Sethi,Qing Kay Li,Lijun Chen,Ben C. Collins,Ludovic C Gillet,Bernd Wollscheid,Hui Zhang,Ruedi Aebersold,Ruedi Aebersold +10 more
TL;DR: The results suggest that N-acylethanolamine acid amidase and protein tyrosine kinase 7 may be used as potential tissue biomarkers to avoid overtreatment of non-aggressive PCa.
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