The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance (Q30844402)

14 October 2017

The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance (English)

1 reference

14 October 2017

1 reference

1 reference

Danielle Thierry-Mieg

object named as

Danielle Thierry-Mieg

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Michele Filosi

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Roberto Visintainer

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Florian Caiment

0 references

Samantha Riccadonna

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Marco Chierici

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Lee J Lancashire

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Binsheng Gong

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Davide Albanese

0 references

Jean Thierry-Mieg

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Giuseppe Jurman

0 references

Jos Kleinjans

1 reference

14 October 2017

Weida Tong

1 reference

14 October 2017

Leming Shi

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14 October 2017

Paweł P Łabaj

1 reference

14 October 2017

Youping Deng

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Andreas Scherer

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Richard S Paules

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Huixiao Hong

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James C Fuscoe

1 reference

14 October 2017

Cesare Furlanello

1 reference

14 October 2017

Marina Bessarabova

1 reference

14 October 2017

Dalila Megherbi

1 reference

14 October 2017

Pierre R Bushel

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14 October 2017

David P Kreil

1 reference

14 October 2017

Joost van Delft

1 reference

14 October 2017

Charles Wang

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14 October 2017

Joshua Xu

1 reference

14 October 2017

Hong Fang

1 reference

14 October 2017

Jie Shen

1 reference

14 October 2017

Zhenqiang Su

1 reference

14 October 2017

Joe Meehan

1 reference

14 October 2017

Xiaojin Li

1 reference

14 October 2017

Lu Yang

1 reference

14 October 2017

Haiqing Li

1 reference

14 October 2017

Stan Gaj

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14 October 2017

Viswanath Devanarayan

1 reference

14 October 2017

Jian Wang

1 reference

14 October 2017

Yong Yang

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14 October 2017

Hui-Rong Qian

1 reference

14 October 2017

Yuri Nikolsky

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14 October 2017

Ke K Zhang

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14 October 2017

Jianying Li

1 reference

14 October 2017

Jui-Hua Hsieh

1 reference

14 October 2017

Daniel L Svoboda

1 reference

14 October 2017

Scott S Auerbach

1 reference

14 October 2017

24 August 2014

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14 October 2017

926-932

1 reference

describes a project that uses

14 October 2017

limma

1 reference

22 June 2022

https://europepmc.org/article/PMC/4243706

based on heuristic

inferred from PubMed Central ID database lookup

cites work

Dynamic expression of 3' UTRs revealed by Poisson hidden Markov modeling of RNA-Seq: implications in gene expression profiling

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4243706

RNA-Seq profiling reveals novel hepatic gene expression pattern in aflatoxin B1 treated rats

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4243706

Comparative RNA-Seq and microarray analysis of gene expression changes in B-cell lymphomas of Canis familiaris.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4243706

Comparative study of RNA-seq- and microarray-derived coexpression networks in Arabidopsis thaliana.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4243706

RNA-Seq vs dual- and single-channel microarray data: sensitivity analysis for differential expression and clustering

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4243706

Revisiting global gene expression analysis

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4243706

A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4243706

A decade of toxicogenomic research and its contribution to toxicological science

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4243706

A systematic comparison and evaluation of high density exon arrays and RNA-seq technology used to unravel the peripheral blood transcriptome of sickle cell disease

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4243706

Gene-expression measurement: variance-modeling considerations for robust data analysis

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4243706

Comparing next-generation sequencing and microarray technologies in a toxicological study of the effects of aristolochic acid on rat kidneys

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4243706

Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4243706

RNA-seq: technical variability and sampling.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4243706

Microarrays, deep sequencing and the true measure of the transcriptome

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4243706

Evaluating gene expression in C57BL/6J and DBA/2J mouse striatum using RNA-Seq and microarrays

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4243706

Human transcriptome array for high-throughput clinical studies.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4243706

RNA sequencing shows no dosage compensation of the active X-chromosome

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4243706

Analysis and design of RNA sequencing experiments for identifying isoform regulation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4243706

Differential expression analysis for sequence count data

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4243706

Ontology-Based Meta-Analysis of Global Collections of High-Throughput Public Data

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4243706

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4243706

Consistency of predictive signature genes and classifiers generated using different microarray platforms.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4243706

A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4243706

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4243706

TopHat: discovering splice junctions with RNA-Seq

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4243706

A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4243706

RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4243706

Mapping and quantifying mammalian transcriptomes by RNA-Seq

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4243706

Rat toxicogenomic study reveals analytical consistency across microarray platforms

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4243706

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4243706

AceView: a comprehensive cDNA-supported gene and transcripts annotation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4243706

Microarray scanner calibration curves: characteristics and implications

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4243706

Development of a large-scale chemogenomics database to improve drug candidate selection and to understand mechanisms of chemical toxicity and action

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4243706

Signal transduction pathway profiling of individual tumor samples

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4243706

Summaries of Affymetrix GeneChip probe level data

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4243706

Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4243706

The TRANSFAC system on gene expression regulation.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4243706

TRANSFAC: an integrated system for gene expression regulation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4243706

Overview of BioCreAtIvE task 1B: normalized gene lists

14 July 2018

1 reference

The External RNA Controls Consortium: a progress report.

21 January 2018

1 reference

Analysis of high density expression microarrays with signed-rank call algorithms

21 January 2018

1 reference

Advancing Regulatory Science

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25150839

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A Model-Based Background Adjustment for Oligonucleotide Expression Arrays

1 reference

inferred from DOI database lookup

7 January 2021

based on heuristic

Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection

1 reference

6 June 2024

https://opencitations.net/index/api/v1/references/10.1038/NBT.3001

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

1 reference

6 June 2024

https://opencitations.net/index/api/v1/references/10.1038/NBT.3001

Identifiers

DOI

10.1038/NBT.3001

1 reference

14 October 2017

1 reference

14 October 2017

PubMed publication ID

25150839

1 reference