On differential variability of expression ratios: improving statistical inference about gene expression changes from microarray data

scientific article

On differential variability of expression ratios: improving statistical inference about gene expression changes from microarray data is …
instance of (P31):
scholarly articleQ13442814

External links are
P8978DBLP publication IDjournals/jcb/NewtonKRBT01
P356DOI10.1089/106652701300099074
P698PubMed publication ID11339905
P5875ResearchGate publication ID11997103

P2093author name stringTsui KW
Blattner FR
Newton MA
Kendziorski CM
Richmond CS
P433issue1
P921main subjectstatisticsQ12483
P304page(s)37-52
P577publication date2001-01-01
P1433published inJournal of Computational BiologyQ6295003
P1476titleOn differential variability of expression ratios: improving statistical inference about gene expression changes from microarray data
P478volume8

Reverse relations

cites work (P2860)
Q58117381A Bayesian Framework for Statistical Inference from Gene Expression Data
Q34533093A Bayesian Model for Pooling Gene Expression Studies That Incorporates Co-Regulation Information
Q51905680A Bayesian mixture model for metaanalysis of microarray studies
Q34362351A Bayesian model for cross-study differential gene expression
Q31045903A MARKOV RANDOM FIELD-BASED APPROACH TO CHARACTERIZING HUMAN BRAIN DEVELOPMENT USING SPATIAL-TEMPORAL TRANSCRIPTOME DATA.
Q31111756A Markov random field model for network-based analysis of genomic data
Q31050289A Markov random field-based approach for joint estimation of differentially expressed genes in mouse transcriptome data
Q30855769A NEW METHOD OF PEAK DETECTION FOR ANALYSIS OF COMPREHENSIVE TWO-DIMENSIONAL GAS CHROMATOGRAPHY MASS SPECTROMETRY DATA
Q33373568A Poisson mixture model to identify changes in RNA polymerase II binding quantity using high-throughput sequencing technology
Q36889657A Statistical Method and Tool to Account for Indirect Calorimetry Differential Measurement Error in a Single-Subject Analysis
Q31162669A case study on choosing normalization methods and test statistics for two-channel microarray data
Q34667581A comparison of background correction methods for two-colour microarrays
Q33289533A comprehensive evaluation of SAM, the SAM R-package and a simple modification to improve its performance
Q27330224A dominantly acting murine allele of Mcm4 causes chromosomal abnormalities and promotes tumorigenesis
Q51578061A flexible and powerful bayesian hierarchical model for ChIP-Chip experiments
Q42776628A full Bayesian hierarchical mixture model for the variance of gene differential expression
Q33810019A functional and transcriptomic analysis of NET1 bioactivity in gastric cancer
Q36586611A gene expression network model of type 2 diabetes links cell cycle regulation in islets with diabetes susceptibility
Q44643284A general method for accurate estimation of false discovery rates in identification of differentially expressed genes
Q33566211A hidden Markov random field model for genome-wide association studies
Q51897625A marginal mixture model for selecting differentially expressed genes across two types of tissue samples.
Q30809573A mixture model approach to detecting differentially expressed genes with microarray data
Q30478833A model of anti-angiogenesis: differential transcriptosome profiling of microvascular endothelial cells from diffuse systemic sclerosis patients
Q33893362A modulated empirical Bayes model for identifying topological and temporal estrogen receptor α regulatory networks in breast cancer.
Q33492779A new class of mixture models for differential gene expression in DNA microarray data
Q34329338A segmental nearest neighbor normalization and gene identification method gives superior results for DNA-array analysis
Q48449906A simple implementation of a normal mixture approach to differential gene expression in multiclass microarrays
Q36083317A statistical framework for expression quantitative trait loci mapping
Q52053666A statistical method for flagging weak spots improves normalization and ratio estimates in microarrays
Q31034018A two-sample Bayesian t-test for microarray data
Q30981916A two-step strategy for detecting differential gene expression in cDNA microarray data
Q42605603A unified approach for simultaneous gene clustering and differential expression identification
Q33812809A virulent strain of deformed wing virus (DWV) of honeybees (Apis mellifera) prevails after Varroa destructor-mediated, or in vitro, transmission
Q39832548ATF3 plays a protective role against toxicity by N-terminal fragment of mutant huntingtin in stable PC12 cell line
Q24797824Accuracy of cDNA microarray methods to detect small gene expression changes induced by neuregulin on breast epithelial cells
Q64120264Accurate and efficient estimation of small p-values with the cross-entropy method: applications in genomic data analysis
Q36981115An Integrative Framework for Bayesian Variable Selection with Informative Priors for Identifying Genes and Pathways
Q24797914An adaptive method for cDNA microarray normalization
Q25257101An approach for clustering gene expression data with error information
Q44876159An empirical Bayes approach for multiple tissue eQTL analysis.
Q40566390An empirical Bayes optimal discovery procedure based on semiparametric hierarchical mixture models
Q42598654An empirical Bayes' approach to joint analysis of multiple microarray gene expression studies.
Q30429288An evolutionarily 'young' lysine residue in histone H3 attenuates transcriptional output in Saccharomyces cerevisiae
Q24814337Analysis of a splice array experiment elucidates roles of chromatin elongation factor Spt4-5 in splicing
Q36731621Analysis of microarray experiments of gene expression profiling.
Q34069993Analyzing 2D gel images using a two-component empirical bayes model
Q35728009Anti-inflammatory agent indomethacin reduces invasion and alters metabolism in a human breast cancer cell line
Q35821854Applications of array technology: melanoma research and diagnosis
Q30660197Argus--a new database system for Web-based analysis of multiple microarray data sets
Q36314706Associating phenotypes with molecular events: recent statistical advances and challenges underpinning microarray experiments
Q34298215Batch correction of microarray data substantially improves the identification of genes differentially expressed in Rheumatoid Arthritis and Osteoarthritis
Q24803156Bayesian analysis of gene expression levels: statistical quantification of relative mRNA level across multiple strains or treatments
Q31014134Bayesian inference with historical data-based informative priors improves detection of differentially expressed genes
Q45966801Bayesian machine learning and its potential applications to the genomic study of oral oncology.
Q31104633Bayesian meta-analysis models for microarray data: a comparative study
Q33242484Bayesian models for pooling microarray studies with multiple sources of replications
Q44395033Bayesian nonparametric variable selection as an exploratory tool for discovering differentially expressed genes
Q51945684Bayesian robust inference for differential gene expression in microarrays with multiple samples
Q92717121Big data differential analysis of microglial cell responses in neurodegenerative diseases
Q38556515Biomarker Discovery Using Statistically Significant Gene Sets
Q36013464Biomechanical Screening of Cell Therapies for Vocal Fold Scar
Q36295725Comparison of statistical methods for subnetwork detection in the integration of gene expression and protein interaction network
Q35463773Comparison of temporal transcriptomic profiles from immature lungs of two rat strains reveals a viral response signature associated with chronic lung dysfunction
Q31032336Comparison of various statistical methods for identifying differential gene expression in replicated microarray data
Q36597671Computational biology: toward deciphering gene regulatory information in mammalian genomes
Q30950304Computational strategies for analyzing data in gene expression microarray experiments
Q33309499Coordinate up-regulation of TMEM97 and cholesterol biosynthesis genes in normal ovarian surface epithelial cells treated with progesterone: implications for pathogenesis of ovarian cancer
Q56887724Current Awareness on Comparative and Functional Genomics
Q34166262DNA microarray experiments: biological and technological aspects
Q30440132Data mining in genomics
Q24813210Decoding the nucleoid organisation of Bacillus subtilis and Escherichia coli through gene expression data
Q43123547Decreased in vivo virulence and altered gene expression by a Brucella melitensis light-sensing histidine kinase mutant
Q91958571Density distribution of gene expression profiles and evaluation of using maximal information coefficient to identify differentially expressed genes
Q36328424Detecting disease-associated genomic outcomes using constrained mixture of Bayesian hierarchical models for paired data
Q31033214Determination of strongly overlapping signaling activity from microarray data.
Q38480915Differential changes in gene expression in human brain during late first trimester and early second trimester of pregnancy
Q30607343Differential expression analysis for paired RNA-Seq data
Q38304630Differential gene expression analysis in antimony-unresponsive Indian kala azar (visceral leishmaniasis) clinical isolates by DNA microarray.
Q30651161Differential gene expression analysis using coexpression and RNA-Seq data
Q37019208Distinct and shared transcriptomes are regulated by microphthalmia-associated transcription factor isoforms in mast cells
Q33817957Ectopic expression of X-linked lymphocyte-regulated protein pM1 renders tumor cells resistant to antitumor immunity
Q35210490Ectopic expression of vascular cell adhesion molecule-1 as a new mechanism for tumor immune evasion
Q24806854Effect of sample size and P-value filtering techniques on the detection of transcriptional changes induced in rat neuroblastoma (NG108) cells by mefloquine
Q36203916Empirical Bayes Model Comparisons for Differential Methylation Analysis
Q51961966Empirical Bayes estimation of demographic schedules for small areas.
Q57314340Empirical Bayes estimation of gene-specific effects in micro-array research
Q56622262Empirical Bayes false coverage rate controlling confidence intervals
Q51281870Empirical Bayes ranking and selection methods via semiparametric hierarchical mixture models in microarray studies
Q46277377Empirical bayes methods and false discovery rates for microarrays
Q24793903Empirical characterization of the expression ratio noise structure in high-density oligonucleotide arrays
Q51091499Empirical comparison of tests for differential expression on time-series microarray experiments
Q36941383Erythritol triggers expression of virulence traits in Brucella melitensis.
Q47373827Estimating Effect Sizes of Differentially Expressed Genes for Power and Sample-Size Assessments in Microarray Experiments
Q33448588Estimating the false discovery rate using mixed normal distribution for identifying differentially expressed genes in microarray data analysis.
Q51906420Estimating the false discovery rate using nonparametric deconvolution
Q30947082Evaluation of differential gene expression in Leishmania major Friedlin procyclics and metacyclics using DNA microarray analysis
Q58456311Experimental Design and Analysis of Microarray Data
Q35362212Exploiting identifiability and intergene correlation for improved detection of differential expression
Q24791182Exploratory differential gene expression analysis in microarray experiments with no or limited replication
Q50704656Extensions to gene set enrichment
Q33947300Extraocular muscle is defined by a fundamentally distinct gene expression profile
Q31143781EzArray: a web-based highly automated Affymetrix expression array data management and analysis system
Q33518493Feature selection and classification of MAQC-II breast cancer and multiple myeloma microarray gene expression data
Q34086288Finding consistent patterns: A nonparametric approach for identifying differential expression in RNA-Seq data
Q48422495Flexible empirical Bayes models for differential gene expression
Q35668719Functional blockade of the voltage-gated potassium channel Kv1.3 mediates reversion of T effector to central memory lymphocytes through SMAD3/p21cip1 signaling
Q44876216Functional genomics and cell wall biosynthesis in loblolly pine
Q30660542GENESHIFT: A Nonparametric Approach for Integrating Microarray Gene Expression Data Based on the Inner Product as a Distance Measure between the Distributions of Genes
Q37175938Gamma-Normal-Gamma mixture model for detecting differentially methylated loci in three breast cancer cell lines
Q28386874Gene Expression Changes in the Olfactory Bulb of Mice Induced by Exposure to Diesel Exhaust Are Dependent on Animal Rearing Environment
Q37202992Gene expression phenotype in heterozygous carriers of ataxia telangiectasia
Q33279846Gene expression profiling of aging reveals activation of a p53-mediated transcriptional program
Q36880133Gene expression profiling of asthma phenotypes demonstrates molecular signatures of atopy and asthma control.
Q34173671Gene selection and classification for cancer microarray data based on machine learning and similarity measures
Q24814852Genome-wide estimation of transcript concentrations from spotted cDNA microarray data
Q35035645Genomic interrogation of mechanism(s) underlying cellular responses to toxicants
Q33509210Graph ranking for exploratory gene data analysis
Q34117556Hedgehog signaling regulates FOXA2 in esophageal embryogenesis and Barrett's metaplasia.
Q28571797Hippocampal gene expression profiling in spatial discrimination learning
Q39888169Hits and misses from gene expression ratio measurements in cDNA microarray studies
Q24793798How many replicates of arrays are required to detect gene expression changes in microarray experiments? A mixture model approach
Q48673697How to understand a complex reality: statistical issues in microarray experiments. Interview by Nadine Lemmens
Q51595301Identification of differentially expressed genes with multivariate outlier analysis
Q33437193Identification of differentially expressed subnetworks based on multivariate ANOVA.
Q30697080Identification of significant features in DNA microarray data
Q34047245Identifying cancer biomarkers by network-constrained support vector machines
Q48515923Identifying differentially expressed genes from microarray experiments via statistic synthesis.
Q44959102Identifying differentially expressed genes in cancer patients using a non‐parameter Ising model
Q36559266Identifying protein interaction subnetworks by a bagging Markov random field-based method.
Q33461968Improved ChIP-chip analysis by a mixture model approach
Q30742391Improved significance test for DNA microarray data: temporal effects of shear stress on endothelial genes
Q42697052Improving Hierarchical Models Using Historical Data with Applications in High-Throughput Genomics Data Analysis
Q24801758Improving identification of differentially expressed genes in microarray studies using information from public databases
Q36481145Improving reliability and performance of DNA microarrays
Q24792834Improving the statistical detection of regulated genes from microarray data using intensity-based variance estimation
Q38957837In vitro effects of extracts of extra virgin olive oil on human colon cancer cells
Q31140186Incorporating gene networks into statistical tests for genomic data via a spatially correlated mixture model
Q36277294Incorporating prior biological knowledge for network-based differential gene expression analysis using differentially weighted graphical LASSO.
Q24798953Incorporation of gene-specific variability improves expression analysis using high-density DNA microarrays
Q34046445Integrated analysis of the heterogeneous microarray data
Q30358866Intensity-based hierarchical Bayes method improves testing for differentially expressed genes in microarray experiments
Q33498713Internal standard-based analysis of microarray data. Part 1: analysis of differential gene expressions
Q39094360Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects
Q33237859LS-NMF: a modified non-negative matrix factorization algorithm utilizing uncertainty estimates
Q83181233Likelihood estimation of conjugacy relationships in linear models with applications to high-throughput genomics
Q50082945Liver gene expression analysis reveals endoplasmic reticulum stress and metabolic dysfunction in SCD1-deficient mice fed a very low-fat diet
Q33960868Loss of stearoyl-CoA desaturase-1 function protects mice against adiposity
Q48358608MMG: a probabilistic tool to identify submodules of metabolic pathways
Q34514417Mapping and analysis of quantitative trait loci in experimental populations
Q33550910Matrix factorisation methods applied in microarray data analysis
Q91691095Maximal information coefficient applied to differentially expressed genes identification: A feasibility study
Q33900400Metabolic Changes in Skin Caused by Scd1 Deficiency: A Focus on Retinol Metabolism
Q37645012Metabolomic Analysis of Liver Tissue from the VX2 Rabbit Model of Secondary Liver Tumors
Q33904600Metabolomics of ApcMin/+ mice genetically susceptible to intestinal cancer
Q31033299Methodological study of affine transformations of gene expression data with proposed robust non-parametric multi-dimensional normalization method
Q33230059Microarray data analysis: from disarray to consolidation and consensus
Q30675927Microarray data quality analysis: lessons from the AFGC project. Arabidopsis Functional Genomics Consortium.
Q47440182Microarray experimental design: power and sample size considerations
Q39616016Microarray optimizations: increasing spot accuracy and automated identification of true microarray signals
Q30662459Microarrays: handling the deluge of data and extracting reliable information
Q30889250Mining microarray data to identify transcription factors expressed in naïve resting but not activated T lymphocytes
Q24802357Model-based cluster analysis of microarray gene-expression data
Q90242516Model-based clustering for identifying disease-associated SNPs in case-control genome-wide association studies
Q24792117Modeling gene expression measurement error: a quasi-likelihood approach
Q30708253Models for microarray gene expression data.
Q29547403Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Q43035275Multiparameter immune profiling of operational tolerance in liver transplantation
Q51264082Multiple Hypothesis Testing: A Methodological Overview
Q52045598Multivariate approach for selecting sets of differentially expressed genes
Q33322221Multivariate hierarchical Bayesian model for differential gene expression analysis in microarray experiments
Q38324237Myc stimulates nuclearly encoded mitochondrial genes and mitochondrial biogenesis
Q33621972Neoplastic transformation of breast epithelial cells by genotoxic stress
Q35362195Nonlinear dependence in the discovery of differentially expressed genes
Q24811281Nonparametric tests for differential gene expression and interaction effects in multi-factorial microarray experiments
Q24815411Normal uniform mixture differential gene expression detection for cDNA microarrays
Q31133081Normal-Gamma-Bernoulli Peak Detection for Analysis of Comprehensive Two-Dimensional Gas Chromatography Mass Spectrometry Data
Q36016824Normalization and analysis of cDNA microarrays using within-array replications applied to neuroblastoma cell response to a cytokine.
Q27860759Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation
Q34049214Normalization, testing, and false discovery rate estimation for RNA-sequencing data
Q33904120Novel application of multi-stimuli network inference to synovial fibroblasts of rheumatoid arthritis patients
Q28755945Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses
Q41962000On correcting the overestimation of the permutation-based false discovery rate estimator
Q73665024On the Kolmogorov-Smirnov Test for Normality with Mean and Variance Unknown
Q36310182Personalized medicine in breast cancer: a systematic review
Q31160218Powerful differential expression analysis incorporating network topology for next-generation sequencing data.
Q79447738Powers of multiple-testing procedures for identification of genes significantly differentially expressed in microarray experiments
Q36310061Prediction of microbial infection of cultured cells using DNA microarray gene-expression profiles of host responses
Q51903805Prenatal exposure to carbon monoxide delays postnatal cardiac maturation
Q30408752Prior robust empirical Bayes inference for large-scale data by conditioning on rank with application to microarray data.
Q64110370Prostate Cancer Gene Regulatory Network Inferred from RNA-Seq Data
Q51592782Ranking analysis for identifying differentially expressed genes
Q33517216Repeated Measurements on Distinct Scales With Censoring-A Bayesian Approach Applied to Microarray Analysis of Maize.
Q42177520Resolution of infection promotes a state of dormancy and long survival of CD4 memory T cells.
Q24806473Resolution of large and small differences in gene expression using models for the Bayesian analysis of gene expression levels and spotted DNA microarrays
Q41341252Robust Significance Analysis of Microarrays by Minimum β-Divergence Method.
Q30939184Robust modeling of differential gene expression data using normal/independent distributions: a Bayesian approach
Q41853518Sebnif: an integrated bioinformatics pipeline for the identification of novel large intergenic noncoding RNAs (lincRNAs)--application in human skeletal muscle cells
Q34563450Signal Oscillation Is Another Reason for Variability in Microarray-Based Gene Expression Quantification
Q47209789Simultaneous inference of phenotype-associated genes and relevant tissues from GWAS data via Bayesian integration of multiple tissue-specific gene networks.
Q30763288Simultaneous inferences based on empirical Bayes methods and false discovery rates ineQTL data analysis
Q34732215Single primer amplification (SPA) of cDNA for microarray expression analysis.
Q35910906Some statistical and regulatory issues in the evaluation of genetic and genomic tests
Q42551836Spiked Dirichlet process prior for Bayesian multiple hypothesis testing in random effects models
Q50666868Spot intensity ratio statistics in two-channel microarray experiments
Q39511410Statistical evaluation of differential expression on cDNA nylon arrays with replicated experiments
Q34669704Statistical issues with microarrays: processing and analysis
Q51216797Statistical mechanics approach to the sample deconvolution problem.
Q37432339Statistical methods for gene set co-expression analysis
Q33638600Statistical methods for integrating multiple types of high-throughput data
Q24796261Statistical methods for ranking differentially expressed genes
Q21194873Statistical tests for differential expression in cDNA microarray experiments
Q37784726Systems genetics, bioinformatics and eQTL mapping.
Q30788588Testing for differentially expressed genes with microarray data
Q34159547The Ume6 regulon coordinates metabolic and meiotic gene expression in yeast
Q33369599The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies
Q24810682The effects of normalization on the correlation structure of microarray data
Q33268949The impact of sample imbalance on identifying differentially expressed genes.
Q64913436The ion channels and transporters gene expression profile indicates a shift in excitability and metabolisms during malignant progression of Follicular Lymphoma.
Q43569601The optimal discovery procedure in multiple significance testing: an empirical Bayes approach
Q58618230The optimal discovery procedure: a new approach to simultaneous significance testing
Q74577790The pros and cons of gene expression analysis by microarrays
Q52045600Thresholding rules for recovering a sparse signal from microarray experiments
Q30651525ToP: A Trend-of-Disease-Progression Procedure Works Well for Identifying Cancer Genes from Multi-State Cohort Gene Expression Data for Human Colorectal Cancer
Q29547575Transactivation of miR-34a by p53 broadly influences gene expression and promotes apoptosis
Q33287248Transcript-level annotation of Affymetrix probesets improves the interpretation of gene expression data
Q44639986Unscaled Bayes factors for multiple hypothesis testing in microarray experiments.
Q37343066Urinary protein profiles in a rat model for diabetic complications
Q44361662Use of a candidate gene array to delineate gene expression patterns in cattle selected for resistance or susceptibility to intestinal nematodes
Q31136974Use of genomic DNA control features and predicted operon structure in microarray data analysis: ArrayLeaRNA - a Bayesian approach
Q47655087Using DNA microarray data to understand the ionizing radiation resistance of Deinococcus radiodurans
Q30998155Using weighted permutation scores to detect differential gene expression with microarray data
Q33752284Validation and characterization of DNA microarray gene expression data distribution and associated moments
Q30676405Variable selection and pattern recognition with gene expression data generated by the microarray technology.
Q24804062Vector algebra in the analysis of genome-wide expression data
Q38079442Where Statistics and Molecular Microarray Experiments Biology Meet
Q24793654Within the fold: assessing differential expression measures and reproducibility in microarray assays.
Q51549832Work efficiency: A new criterion for comprehensive comparison and evaluation of statistical methods in large-scale identification of differentially expressed genes
Q34309083β-empirical Bayes inference and model diagnosis of microarray data

Search more.