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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Cadmium triggers an integrated reprogramming of the metabolism of Synechocystis PCC6803, under the control of the Slr1738 regulator
Laetitia Houot,Martin Floutier,Martin Floutier,Benoit Marteyn,Magali Michaut,Antoine Picciocchi,Pierre Legrain,Pierre Legrain,Jean-Christophe Aude,Corinne Cassier-Chauvat,Corinne Cassier-Chauvat,Franck Chauvat +11 more
TL;DR: In this paper, the authors investigated the global responses to Cadmium and other relevant stresses (H2O2 and Fe) in the model cyanobacterium Synechocystis PCC6803.
Journal ArticleDOI
Identification of overexpressed genes in hepatocellular carcinoma, with special reference to ubiquitin-conjugating enzyme E2C gene expression.
Keisuke Ieta,Keisuke Ieta,Eiki Ojima,Fumiaki Tanaka,Yoshito Nakamura,Naotsugu Haraguchi,Koshi Mimori,Hiroshi Inoue,Hiroyuki Kuwano,Masaki Mori +9 more
TL;DR: The Ube2c gene appeared to be associated with HCC progression, and may be useful as a prognostic indicator for HCC patients and an independent prognostic factor for disease‐free survival rate in multivariate analysis.
Journal ArticleDOI
Reduced Expression of the Insulin Receptor in Mouse Insulinoma (MIN6) Cells Reveals Multiple Roles of Insulin Signaling in Gene Expression, Proliferation, Insulin Content, and Secretion
Mitsuru Ohsugi,Corentin Cras-Méneur,Yiyong Zhou,Ernesto Bernal-Mizrachi,James D. Johnson,Dan S. Luciani,Kenneth S. Polonsky,M. Alan Permutt +7 more
TL;DR: Important roles of the insulin receptor in islet β cell gene expression and function are demonstrated and may serve to elucidate molecular defects in animal models with diminished β cell insulin signaling.
Journal ArticleDOI
Experiments using microarray technology: limitations and standard operating procedures.
TL;DR: This paper outlines standard operating procedures, which help streamline the analysis of microarray data resulting from a diversity of array formats and biological systems, and highlights salient features to provide initial guidance in terms of pitfalls in planning and executing array projects.
Journal ArticleDOI
Exosomes Derived From Pancreatic Stellate Cells: MicroRNA Signature and Effects on Pancreatic Cancer Cells.
Tetsuya Takikawa,Atsushi Masamune,Naoki Yoshida,Shin Hamada,Takayuki Kogure,Tooru Shimosegawa +5 more
TL;DR: The microRNA expression profile in PSC-derived exosomes was clarified and might play a role in the interactions between PSCs and pancreatic cancer cells.
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