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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The seventh layer of the clinical-genomics information infrastructure
Amnon Shabo,Dolev Dotan +1 more
TL;DR: This paper describes how challenges are addressed by Clinical Genomics Level Seven (CGL7), a set of Web services for clinical-genomics decision-support applications that follow the HL7® (Health Level 7®) clinical Genomics standard for the representation and exchange of clinical genomics data.
Journal ArticleDOI
BRD4 promotes metastatic potential in oral squamous cell carcinoma through the epigenetic regulation of the MMP2 gene.
Tatsuro Yamamoto,Akiyuki Hirosue,Masafumi Nakamoto,Ryoji Yoshida,Junki Sakata,Yuichiro Matsuoka,Kenta Kawahara,Yuka Nagao,Masashi Nagata,Nozomu Takahashi,Akimitsu Hiraki,Masanori Shinohara,Mitsuyoshi Nakao,Noriko Saitoh,Hideki Nakayama +14 more
TL;DR: BRD4 contributes to metastasis in OSCC, through the epigenetic regulation of the MMP2 gene, and thus BRD4 may represent a therapeutic target and a novel prediction indicator for metastasis.
Journal ArticleDOI
Selection of Suitable Reference Genes for RT-qPCR Normalization under Abiotic Stresses and Hormone Stimulation in Persimmon (Diospyros kaki Thunb)
TL;DR: The results showed that the most suitable reference genes across all samples were UBC and GAPDH, and not the commonly used persimmon reference gene ACT, and suggested that it is necessary to choose appropriate reference genes according to the test materials or experimental conditions.
Journal ArticleDOI
BABAR: an R package to simplify the normalisation of common reference design microarray-based transcriptomic datasets
TL;DR: BABAR is an easy-to-use software tool, simplifying the simultaneous normalisation of heterogeneous two-colour common reference design cDNA microarray-based transcriptomic datasets and is the ideal tool to facilitate the identification of differentially expressed genes or network inference analysis from transcriptomic dataset.
Journal ArticleDOI
Effects of urinary and recombinant gonadotrophins on gene expression profiles during the murine peri-implantation period
Rosana M Sibug,Nicole A. Datson,A. M. I. Tijssen,M.C. Morsink,J. de Koning,E.R. de Kloet,Frans M. Helmerhorst +6 more
TL;DR: Urinary gonadotrophins differentially up-regulated the expression of 30 genes, increased resorption and reduced litter size, whereas recombinant gonadOTrophins did not, and might contribute to improve protocols for COS, leading to higher successful pregnancy rates.
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