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
Comparison of microarray-based mRNA profiling technologies for identification of psychiatric disease and drug signatures.
Linda W. Jurata,Yury V. Bukhman,Vinod Charles,Frank Capriglione,Jeffrey Bullard,Andrew L. Lemire,Ali Mohammed,Quyen Pham,Pascal Laeng,Jeffrey A. Brockman,C. Anthony Altar +10 more
TL;DR: The gene expression profiles of human postmortem parietal and prefrontal cortex samples of normal controls and patients with bipolar disease, or human neuroblastoma flat cells treated with the mood-stabilizing drug, valproate, were used to compare the performance of Affymetrix oligonucleotide U133A GeneChips and Agilent Human 1 cDNA microarrays.
Journal ArticleDOI
IL-6/STAT3 Plays a Regulatory Role in the Interaction Between Pancreatic Stellate Cells and Cancer Cells
TL;DR: IL-6/STAT3 pathway regulates the PSC-induced EMT and alterations in gene expression in pancreatic cancer cells and is inhibited by anti- IL-6 antibody or a STAT3 inhibitor.
Journal ArticleDOI
A Tiling Microarray Expression Analysis of Rice Chromosome 4 Suggests a Chromosome-Level Regulation of Transcription
Yuling Jiao,Peixin Jia,Xiangfeng Wang,Ning Su,Ning Su,Shuliang Yu,Dongfen Zhang,Ligeng Ma,Ligeng Ma,Qi Feng,Zhaoqing Jin,Lei Li,Yongbiao Xue,Zhukuan Cheng,Hongyu Zhao,Bin Han,Xing Wang Deng +16 more
TL;DR: An analysis of the transcriptional activity of rice chromosome 4 using a tiling path microarray based on PCR-generated genomic DNA fragments suggests a close correlation between transcriptionalactivity and chromosome organization and the developmental regulation of transcription activity at the chromosome level.
Journal ArticleDOI
Loss of eIF4E Phosphorylation Engenders Depression-like Behaviors via Selective mRNA Translation.
Inês S. Amorim,Sonal Kedia,Stella Kouloulia,Konstanze Simbriger,Ilse Gantois,Seyed Mehdi Jafarnejad,Yupeng Li,Agniete Kampaite,Tine Pooters,Nicola Romanò,Christos G. Gkogkas +10 more
TL;DR: It is demonstrated that ablation of eIF4E phosphorylation in male mice (4Eki mice) does not impair long-term spatial or contextual fear memory, or the late phase of LTP, and a novel phospho-eif4E-dependent translational control mechanism in the brain is proposed, via the GAIT complex (gamma IFN activated inhibitor of translation).
Patent
Non-invasive determination of methylome of fetus or tumor from plasma
TL;DR: In this article, the authors used tissue-specific alleles to identify DNA from the fetus/tumor when the sample has a mixture of DNA and determined the methylation profile by determining a size parameter of a size distribution of DNA fragments.
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