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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Overexpression of PFTK1 predicts resistance to chemotherapy in patients with oesophageal squamous cell carcinoma.
Hiromichi Miyagaki,Makoto Yamasaki,Hiroshi Miyata,Tsuyoshi Takahashi,Yukinori Kurokawa,Kiyokazu Nakajima,S. Takiguchi,Yoshiyuki Fujiwara,Hideshi Ishii,Fumiaki Tanaka,Masaki Mori,Yuichiro Doki +11 more
TL;DR: PFTK1 is not only useful as a prognostic marker, but also as a predictor of the response to chemotherapy.
Journal ArticleDOI
Folate-regulated changes in gene expression in the anterior neural tube of folate binding protein-1 (Folbp1)-deficient murine embryos.
TL;DR: Using antisense RNA amplification and cDNA microarrays, the expression of approximately 5700 genes in the anterior neural tube of gestational day 9 Folbp1−/− embryos that were supplemented with folinic acid were examined and genes that appear to be folate regulated were examined.
Atlas of Genetics and Cytogenetics in Oncology and Haematology
TL;DR: D40/CASC5 mRNA expression is dominant in normal human testis and slight expression are observed in other organs, such as placenta, and at least two alternative isoforms of cDNA were identified.
Journal ArticleDOI
Selection and validation of garlic reference genes for quantitative real-time PCR normalization
Min Liu,Zhen Wu,Fangling Jiang +2 more
TL;DR: The results demonstrated that TUA, GAPDH, UBQ, CYP, and ACT are the most suitable of the eight reference genes for different garlic genotypes, organs, developmental stages, abiotic stresses and media treatments, respectively.
Journal ArticleDOI
Modeling Selective Elimination of Quiescent Cancer Cells from Bone Marrow
Stephen P. Cavnar,Andrew D. Rickelmann,Kaille F. Meguiar,Annie Xiao,Joseph Dosch,Brendan M. Leung,Sasha Cai Lesher-Perez,Shashank Chitta,Kathryn E. Luker,Shuichi Takayama,Gary D. Luker +10 more
TL;DR: A new 384-well 3D spheroid model is established in which small numbers of cancer cells reversibly arrest in G1/G0 phase of the cell cycle when cultured with bone marrow stromal cells, establishing a novel screening platform for therapies that selectively target quiescent tumor cells, facilitating identification of new drugs to prevent recurrent cancer.
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