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
Citations
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The transcriptional response to oxidative stress during vertebrate development: effects of tert-butylhydroquinone and 2,3,7,8-tetrachlorodibenzo-p-dioxin.
Mark E. Hahn,Andrew G. McArthur,Sibel I. Karchner,Diana G. Franks,Matthew J. Jenny,Alicia R. Timme-Laragy,John J. Stegeman,Bruce R. Woodin,Michael J. Cipriano,Elwood Linney +9 more
TL;DR: Data show that zebrafish embryos are responsive to oxidative stress as early as 1 dpf, that responsiveness varies with development in a gene-specific manner, and that the oxidative stress response is substantially conserved in vertebrate animals.
Journal ArticleDOI
Glucose and insulin treatment of insulinoma cells results in transcriptional regulation of a common set of genes
Mitsuru Ohsugi,Corentin Cras-Méneur,Yiyong Zhou,Wesley C. Warren,Ernesto Bernal-Mizrachi,M. Alan Permutt +5 more
TL;DR: Data demonstrate that glucose and insulin rapidly activate a PI 3-kinase pathway, resulting in transcription of a common set of genes, consistent with glucose activation of gene transcription either directly or indirectly through a paracrine/autocrine effect via insulin release.
Journal ArticleDOI
Differential effects of substrate modulus on human vascular endothelial, smooth muscle, and fibroblastic cells.
Karyn G. Robinson,Ting Nie,Aaron D. Baldwin,Elaine C. Yang,Kristi L. Kiick,Kristi L. Kiick,Robert E. Akins +6 more
TL;DR: It is suggested that the growth of multiple vascular cell types can be supported by PEG hydrogels and that different populations can be controlled by altering the mechanical properties of biomaterials.
Journal ArticleDOI
Differential gene expression analysis in antimony-unresponsive Indian kala azar (visceral leishmaniasis) clinical isolates by DNA microarray
Neeloo Singh,Renato Rodrigues de Almeida,Hema Kothari,Pranav Kumar,Gautam Mandal,Mitali Chatterjee,S. Venkatachalam,M. K. Govind,S. K. Mandal,Shyam Sundar +9 more
TL;DR: The results suggest that isolate 39 could have developed resistance by an increased multidrug resistance protein (MRP)-like pump, and provides preliminary clues to the role of a thiol-dependent efflux system in antimonial resistant clinical isolates of Leishmania donovani.
Journal ArticleDOI
Unraveling gene function in agricultural species using gene co-expression networks.
TL;DR: Grotewold et al. as mentioned in this paper reviewed fundamental concepts in the construction and application of co-expression networks with a focus on agricultural crops and provided perspective on important considerations that arise when analyzing network relationships.
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