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
Combined zebrafish-yeast chemical-genetic screens reveal gene-copper-nutrition interactions that modulate melanocyte pigmentation.
Hironori Ishizaki,Michaela Spitzer,Jan Wildenhain,Corina Anastasaki,Zhiqiang Zeng,Sonam Dolma,Michael Shaw,Erik C. Madsen,Jonathan D. Gitlin,Richard Marais,Mike Tyers,E. Elizabeth Patton +11 more
TL;DR: Zebrafish-yeast screening method combines the power of zebrafish as a disease model with facile genome-scale identification of chemical-genetic interactions in yeast to enable the discovery and dissection of complex multigenic interactions in disease-gene networks.
Journal ArticleDOI
Gene expression responses of paper birch (Betula papyrifera) to elevated CO2 and O3 during leaf maturation and senescence.
Sari Kontunen-Soppela,Sari Kontunen-Soppela,Juha Parviainen,Hanna Ruhanen,Mikael Brosché,Markku Keinänen,Ramesh Thakur,Mikko Kolehmainen,Jaakko Kangasjärvi,Elina Oksanen,David F. Karnosky,Elina Vapaavuori +11 more
TL;DR: Gene expression responses of paper birch leaves to elevated concentrations of CO(2) and O(3) were studied with microarray analyses from three time points during the summer of 2004 at Aspen FACE, indicating that CO(1) cannot totally alleviate the harmful effects of O(2), and combined treatment resulted in differential gene expression.
Journal ArticleDOI
Detecting Microbial Dysbiosis Associated with Pediatric Crohn Disease Despite the High Variability of the Gut Microbiota
Feng Wang,Jess L. Kaplan,Benjamin D. Gold,Manoj Bhasin,Naomi L. Ward,Richard Kellermayer,Barbara S. Kirschner,Melvin B. Heyman,Scot E. Dowd,Stephen B. Cox,Haluk Dogan,Blaire Steven,George D. Ferry,Stanley A. Cohen,Robert N. Baldassano,Christopher J. Moran,Elizabeth A. Garnett,Lauren Drake,Hasan H. Otu,Leonid A. Mirny,Towia A. Libermann,Harland S. Winter,Kirill S. Korolev +22 more
TL;DR: In this paper, a set of techniques based on population dynamics and information theory was developed to identify additional bacterial taxa associated with pediatric Crohn disease and can detect significant changes in microbial communities with fewer samples than previous statistical approaches required.
BookDOI
Macrophages: Biology and role in the pathology of diseases
TL;DR: The origin, Activation and Polarization of macrophages, and the role of microRNA in macrophage activation and polarization, are discussed.
Journal ArticleDOI
The genetic dissection of immune response using gene-expression studies and genome mapping
TL;DR: In the recently proposed 'genetical genomics' framework, members of a segregating population are characterised for genome-wide molecular markers and for gene expression levels which facilitates the mapping of expression-QTL (eQTL): loci in the genome that control the expression of genes.
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