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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Journal ArticleDOI
Effects of proteasome inhibitor MG-132 on the parasite Schistosoma mansoni.
Enyara Rezende Morais,Katia C. Oliveira,Katia C. Oliveira,Renato Graciano de Paula,Alice M.M. Ornelas,Érika B. C. Moreira,Fernanda Rafacho Badoco,Lizandra Guidi Magalhães,Sergio Verjovski-Almeida,Sergio Verjovski-Almeida,Vanderlei Rodrigues +10 more
TL;DR: The genome-wide changes in gene expression of S. mansoni adult worms exposed in vitro to MG-132 suggest that the proteasome might be an important molecular target for the design of new drugs against schistosomiasis.
Journal ArticleDOI
Multistrain Genetic Comparisons Reveal CCR5 as a Receptor Involved in Airway Hyperresponsiveness
Julia K. L. Walker,Adriana Ahumada,Bryan C. Frank,Renee Gaspard,Katherine G. Berman,John Quackenbush,David A. Schwartz +6 more
TL;DR: Using DNA microarrays and knock-out mouse studies, it is shown that CCR5 plays a definitive role in the development of ovalbumin-induced allergic airway inflammatory disease.
Journal ArticleDOI
Deblender: a semi-/unsupervised multi-operational computational method for complete deconvolution of expression data from heterogeneous samples.
Konstantina Dimitrakopoulou,Elisabeth Wik,Elisabeth Wik,Lars A. Akslen,Lars A. Akslen,Inge Jonassen +5 more
TL;DR: Deblender is presented, a flexible complete deconvolution tool operating in semi−/unsupervised mode based on the user’s access to known marker gene lists and information about cell/tissue composition that corroborate that Deblender can be a valuable tool to improve understanding of gene expression datasets with implications for prediction and clinical utilization.
Posted Content
Orchestrating the Development Lifecycle of Machine Learning-Based IoT Applications: A Taxonomy and Survey
Bin Qian,Jie Su,Zhenyu Wen,Devki Nandan Jha,Yinhao Li,Yu Guan,Deepak Puthal,Philip James,Renyu Yang,Albert Y. Zomaya,Omer Rana,Lizhe Wang,Maciej Koutny,Rajiv Ranjan +13 more
TL;DR: This article provides a comprehensive and systematic survey of the development lifecycle of ML-based IoT applications and outlines the core roadmap and taxonomy and assess and compare existing standard techniques used at individual stages.
Journal ArticleDOI
Microarray analysis reveals that high mobility group A1 is involved in colorectal cancer metastasis.
Yusuke Takahashi,Genta Sawada,Tetsuya Sato,Junji Kurashige,Kosuke Mima,Tae Matsumura,Ryutaro Uchi,Hiroki Ueo,Masahisa Ishibashi,Yuki Takano,Sayuri Akiyoshi,Hidetoshi Eguchi,Tomoya Sudo,Keishi Sugimachi,Jun Ichi Tanaka,Shin-ei Kudo,Yuichiro Doki,Masaki Mori,Koshi Mimori +18 more
TL;DR: The present study strongly supports the clinical significance of HMGA1 expression as a predictive indicator of lymph node metastasis in CRC cases, even in submucosal invasive cases which could be cured by local resection.
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