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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Journal ArticleDOI
Gene expression profiling of the androgen receptor antagonists flutamide and vinclozolin in zebrafish (Danio rerio) gonads
Dalma Martinović-Weigelt,Rong-Lin Wang,Daniel L. Villeneuve,David C. Bencic,James M. Lazorchak,Gerald T. Ankley +5 more
TL;DR: It is found that VZ and FLU potentially impact reproductive processes via multiple pathways related to steroidogenesis, spermatogenesis, and fertilization, as demonstrated by overlap in differentially-expressed genes and enrichment of several common key pathways.
Journal ArticleDOI
Microarray analysis in pulmonary hypertension.
TL;DR: To date, numerous human microarray studies have been conducted to analyse global (lung homogenate samples), compartment-specific (laser capture microdissection), cell type-specific and circulating cell (peripheral blood) expression profiles, and Combined, they provide important information on development, progression and the end-stage disease.
Journal ArticleDOI
Image analysis tools and emerging algorithms for expression proteomics
Andrew W. Dowsey,Jane A. English,Frédérique Lisacek,Jeffrey S. Morris,Guang-Zhong Yang,Michael J. Dunn +5 more
TL;DR: The image analysis pipeline for the established 2‐DE technique of protein separation is described, and by first covering signal analysis for MS, the current image analysis workflow for the emerging high‐throughput ‘shotgun’ proteomics platform of LC coupled to MS (LC/MS).
Journal ArticleDOI
Identification of a gene-pathway associated with non-alcoholic steatohepatitis.
Angel Rubio,Elizabeth Guruceaga,Mercedes Vazquez-Chantada,Juan Sandoval,L. Alfonso Martínez-Cruz,Victor Segura,José L. Sevilla,Adam Podhorski,Fernando J. Corrales,Luis Enrique Nores Torres,Manuel S. Rodriguez,Fabienne Aillet,Usue Ariz,Felix Martínez Arrieta,Juan Caballería,Antonio Martín-Duce,Shelly C. Lu,M. Luz Martínez-Chantar,José M. Mato +18 more
TL;DR: It is speculated that hyperphosphorylation of Sp1 may be involved in the genesis of steatosis and that other factors, such as oxidative stress, may trigger its progression to NASH.
Journal ArticleDOI
Intensity‐based analysis of two‐colour microarrays enables efficient and flexible hybridization designs
Peter A C 't Hoen,Rolf Turk,Judith M. Boer,Ellen Sterrenburg,Renée X. de Menezes,Gert-Jan B. van Ommen,Johan T. den Dunnen +6 more
TL;DR: It is found that the signal intensity of the cRNA targets was not influenced by the presence of a target labelled in the opposite colour, which indicates that targets do not compete for binding sites on the array, which is essential for intensity-based analysis.
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