(Q31160471)

19 September 2017

A weighted average difference method for detecting differentially expressed genes from microarray data (English)

1 reference

19 September 2017

Koji Kadota

1

0 references

author name string

Yuji Nakai

series ordinal

2

1 reference

19 September 2017

Kentaro Shimizu

series ordinal

3

1 reference

19 September 2017

language of work or name

English

0 references

publication date

26 June 2008

1 reference

Algorithms for Molecular Biology

19 September 2017

1 reference

19 September 2017

3

1 reference

19 September 2017

1

0 references

page(s)

8

1 reference

Creative Commons Attribution 2.0 Generic

19 September 2017

start time

26 June 2008

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

1 reference

April 2022 Public Data File from Crossref

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A discussion concerning the inclusion of variety effect when analysis of variance is used to detect differentially expressed genes.

21 June 2018

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Evaluation of two outlier-detection-based methods for detecting tissue-selective genes from microarray data

21 June 2018

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21 June 2018

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DNA methyltransferase 3B (DNMT3B) mutations in ICF syndrome lead to altered epigenetic modifications and aberrant expression of genes regulating development, neurogenesis and immune function.

21 June 2018

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21 June 2018

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Secreted frizzled-related protein 1 loss contributes to tumor phenotype of clear cell renal cell carcinoma

21 June 2018

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The utility of MAS5 expression summary and detection call algorithms

21 June 2018

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Human X-box binding protein-1 confers both estrogen independence and antiestrogen resistance in breast cancer cell lines.

21 June 2018

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A comprehensive evaluation of SAM, the SAM R-package and a simple modification to improve its performance

21 June 2018

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Microarray analysis of glial cells resistant to JCV infection suggests a correlation between viral infection and inflammatory cytokine gene expression

21 June 2018

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GOGOT: a method for the identification of differentially expressed fragments from cDNA-AFLP data

21 June 2018

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A proposed mechanism for the protective effect of dioxin against breast cancer

21 June 2018

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Inadequate protein intake affects skeletal muscle transcript profiles in older humans

21 June 2018

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Recursive cluster elimination (RCE) for classification and feature selection from gene expression data

21 June 2018

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TXNIP regulates peripheral glucose metabolism in humans

21 June 2018

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Fisher's combined p-value for detecting differentially expressed genes using Affymetrix expression arrays

21 June 2018

1 reference

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The human reticulocyte transcriptome

21 June 2018

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An improved nonparametric approach for detecting differentially expressed genes with replicated microarray data

21 June 2018

1 reference

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Detecting differential expression in microarray data: comparison of optimal procedures

21 June 2018

1 reference

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Distinct transcriptional profiles in ex vivo CD4+ and CD8+ T cells are established early in human immunodeficiency virus type 1 infection and are characterized by a chronic interferon response as well as extensive transcriptional changes in CD8+ T c

21 June 2018

1 reference

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The impact of sample imbalance on identifying differentially expressed genes.

21 June 2018

1 reference

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Early cutaneous gene transcription changes in adult atopic dermatitis and potential clinical implications

21 June 2018

1 reference

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Intensity-based hierarchical Bayes method improves testing for differentially expressed genes in microarray experiments

21 June 2018

1 reference

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NCBI GEO: mining tens of millions of expression profiles--database and tools update

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

A summarization approach for Affymetrix GeneChip data using a reference training set from a large, biologically diverse database

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Identifying genes that contribute most to good classification in microarrays

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

A powerful method for detecting differentially expressed genes from GeneChip arrays that does not require replicates

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Microarray analysis of BeWo and JEG3 trophoblast cell lines: identification of differentially expressed transcripts

21 June 2018

1 reference

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ROKU: a novel method for identification of tissue-specific genes

21 June 2018

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Glucocorticoid receptor activation signals through forkhead transcription factor 3a in breast cancer cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Linear models and empirical bayes methods for assessing differential expression in microarray experiments

21 June 2018

1 reference

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Fibroblast remodeling activity at two- and three-dimensional collagen-glycosaminoglycan interfaces.

21 June 2018

1 reference

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Bayesian modeling of differential gene expression

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

A new summarization method for Affymetrix probe level data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Gene expression profiling reveals intrinsic differences between T-cell acute lymphoblastic leukemia and T-cell lymphoblastic lymphoma.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Rank-based methods as a non-parametric alternative of the T-statistic for the analysis of biological microarray data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Functional analysis of human hematopoietic stem cell gene expression using zebrafish

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Cross-platform comparability of microarray technology: intra-platform consistency and appropriate data analysis procedures are essential

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Functional profiling of human atrial and ventricular gene expression

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Reprogramming of the human atrial transcriptome in permanent atrial fibrillation: expression of a ventricular-like genomic signature.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Rank Difference Analysis of Microarrays (RDAM), a novel approach to statistical analysis of microarray expression profiling data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Bioconductor: open software development for computational biology and bioinformatics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Association between gene expression profile and tumor invasion in oral squamous cell carcinoma

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Gene selection and classification from microarray data using kernel machine

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Genome-scale expression profiling of Hutchinson-Gilford progeria syndrome reveals widespread transcriptional misregulation leading to mesodermal/mesenchymal defects and accelerated atherosclerosis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Genomic profiling of the human heart before and after mechanical support with a ventricular assist device reveals alterations in vascular signaling networks.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Three-parameter lognormal distribution ubiquitously found in cDNA microarray data and its application to parametric data treatment

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Exploration, normalization, and summaries of high density oligonucleotide array probe level data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Detection of genes with tissue-specific expression patterns using Akaike's information criterion procedure

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Microarray data normalization and transformation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

The limit fold change model: a practical approach for selecting differentially expressed genes from microarray data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Gene selection for sample classification based on gene expression data: study of sensitivity to choice of parameters of the GA/KNN method

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Analysis of strain and regional variation in gene expression in mouse brain

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Analysis of variance for gene expression microarray data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Significance analysis of microarrays applied to the ionizing radiation response

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Gene ontology: tool for the unification of biology

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Computational methods for the identification of differential and coordinated gene expression.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Gene expression profiling in the adult Down syndrome brain.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

RefPlus: an R package extending the RMA Algorithm.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Improving the power to detect differentially expressed genes in comparative microarray experiments by including information from self-self hybridizations.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Accurate ranking of differentially expressed genes by a distribution-free shrinkage approach.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Gene selection with multiple ordering criteria

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Flexible empirical Bayes models for differential gene expression

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Gene expression analysis of bipolar disorder reveals downregulation of the ubiquitin cycle and alterations in synaptic genes

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Partition resampling and extrapolation averaging: approximation methods for quantifying gene expression in large numbers of short oligonucleotide arrays

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Increased expression of Wnt5a in psoriatic plaques.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Bayesian robust inference for differential gene expression in microarrays with multiple samples.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Comparison of Affymetrix GeneChip expression measures.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Skeletal muscle gene expression profiling in mitochondrial disorders.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Use of within-array replicate spots for assessing differential expression in microarray experiments

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Valproate-induced alterations in human theca cell gene expression: clues to the association between valproate use and metabolic side effects

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Detection of cardiac allograft rejection and response to immunosuppressive therapy with peripheral blood gene expression.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Identifying differentially expressed genes from microarray experiments via statistic synthesis.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Gene expression profiling of human lung tissue from smokers with severe emphysema.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

A benchmark for Affymetrix GeneChip expression measures

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Robust estimators for expression analysis

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Empirical bayes methods and false discovery rates for microarrays

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

Gene expression profiling in the early phases of DMD: a constant molecular signature characterizes DMD muscle from early postnatal life throughout disease progression

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

A distribution free summarization method for Affymetrix GeneChip(R) arrays

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2464587

ROC curves are a suitable and flexible tool for the analysis of gene expression profiles

31 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18578891

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

TNF induces distinct gene expression programs in microvascular and macrovascular human endothelial cells

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18578891

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1748-7188-3-8

1 reference

journals/almob/KadotaNS08

19 September 2017

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

1 reference

9 September 2019

https://scigraph.springernature.com/pub.10.1186/1748-7188-3-8

1 reference

19 September 2017

PubMed publication ID

18578891

1 reference