(Q34897615)

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Transfer of clinically relevant gene expression signatures in breast cancer: from Affymetrix microarray to Illumina RNA-Sequencing technology

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Europe PubMed Central

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5 August 2017

Transfer of clinically relevant gene expression signatures in breast cancer: from Affymetrix microarray to Illumina RNA-Sequencing technology (English)

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Europe PubMed Central

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5 August 2017

Benjamin Haibe-Kains

16

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Benjamin Haibe-Kains

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David Brown

3

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Christine Desmedt

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Christine Desmedt

4

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Stefan Michiels

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Stefan Michiels

6

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Christos Sotiriou

15

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Christos Sotiriou

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5 August 2017

Françoise Rothé

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Françoise Rothé

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5 August 2017

Denis Larsimont

10

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Denis Larsimont

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5 August 2017

Roberto C Salgado-Delgado

9

object named as

Roberto Salgado

1 reference

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5 August 2017

8

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Samira Majjaj

1 reference

Europe PubMed Central

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5 August 2017

Michail Ignatiadis

11

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Michail Ignatiadis

1 reference

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5 August 2017

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Debora Fumagalli

1

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5 August 2017

Alexis Blanchet-Cohen

2

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5 August 2017

David Gacquer

5

1 reference

Europe PubMed Central

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5 August 2017

Marion Maetens

12

1 reference

Europe PubMed Central

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5 August 2017

Martine Piccart

13

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5 August 2017

Vincent Detours

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5 August 2017

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publication date

21 November 2014

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5 August 2017

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5 August 2017

15

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5 August 2017

1008

1 reference

Europe PubMed Central

PubMed publication ID

5 August 2017

Recommendations for human epidermal growth factor receptor 2 testing in breast cancer: American Society of Clinical Oncology/College of American Pathologists clinical practice guideline update

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

Large scale comparison of gene expression levels by microarrays and RNAseq using TCGA data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

Personalizing the treatment of women with early breast cancer: highlights of the St Gallen International Expert Consensus on the Primary Therapy of Early Breast Cancer 2013

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

Maize gene atlas developed by RNA sequencing and comparative evaluation of transcriptomes based on RNA sequencing and microarrays

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

A three-gene model to robustly identify breast cancer molecular subtypes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

Characterization and clinical evaluation of CD10+ stroma cells in the breast cancer microenvironment

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

Jetset: selecting the optimal microarray probe set to represent a gene

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

GeneSigDB: a manually curated database and resource for analysis of gene expression signatures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

Bias detection and correction in RNA-Sequencing data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

Microarrays, deep sequencing and the true measure of the transcriptome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

Computational methods for transcriptome annotation and quantification using RNA-seq

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

BamTools: a C++ API and toolkit for analyzing and managing BAM files

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

RNA sequencing: advances, challenges and opportunities

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

Minimising immunohistochemical false negative ER classification using a complementary 23 gene expression signature of ER status

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

American Society of Clinical Oncology/College of American Pathologists guideline recommendations for immunohistochemical testing of estrogen and progesterone receptors in breast cancer (unabridged version).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

PIK3CA mutations associated with gene signature of low mTORC1 signaling and better outcomes in estrogen receptor-positive breast cancer

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

Statistical design and analysis of RNA sequencing data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

Understanding mechanisms underlying human gene expression variation with RNA sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

Transcriptome genetics using second generation sequencing in a Caucasian population

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

Frozen robust multiarray analysis (fRMA).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

Microarray-based determination of estrogen receptor, progesterone receptor, and HER2 receptor status in breast cancer

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

Estimating accuracy of RNA-Seq and microarrays with proteomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

Gene-expression signatures in breast cancer

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

Supervised risk predictor of breast cancer based on intrinsic subtypes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

RNA-Seq: a revolutionary tool for transcriptomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

Insulin-like growth factor-I activates gene transcription programs strongly associated with poor breast cancer prognosis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

Meta-analysis of gene expression profiles in breast cancer: toward a unified understanding of breast cancer subtyping and prognosis signatures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

Mapping and quantifying mammalian transcriptomes by RNA-Seq

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

The transcriptional landscape of the yeast genome defined by RNA sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

Clinical application of the 70-gene profile: the MINDACT trial

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

Molecular subtypes in breast cancer evaluation and management: divide and conquer

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

Challenges in projecting clustering results across gene expression-profiling datasets

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

American Society of Clinical Oncology 2007 update of recommendations for the use of tumor markers in breast cancer

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

An immune response gene expression module identifies a good prognosis subtype in estrogen receptor negative breast cancer

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

Poor prognosis in carcinoma is associated with a gene expression signature of aberrant PTEN tumor suppressor pathway activity.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

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

1 reference

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8 July 2018

Reproducible research: a bioinformatics case study

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8 July 2018

The molecular portraits of breast tumors are conserved across microarray platforms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

Activation of mitogen-activated protein kinase in estrogen receptor alpha-positive breast cancer cells in vitro induces an in vivo molecular phenotype of estrogen receptor alpha-negative human breast tumors

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis

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8 July 2018

Oncogenic pathway signatures in human cancers as a guide to targeted therapies

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8 July 2018

BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

Breast cancer classification and prognosis based on gene expression profiles from a population-based study

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4289354

8 July 2018

Repeated observation of breast tumor subtypes in independent gene expression data sets

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8 July 2018

Gene expression profiling predicts clinical outcome of breast cancer

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8 July 2018

Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications

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8 July 2018

Molecular portraits of human breast tumours

1 reference

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8 July 2018

The application of DNA microarrays in gene expression analysis.

1 reference

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8 July 2018

A new molecular predictor of distant recurrence in ER-positive, HER2-negative breast cancer adds independent information to conventional clinical risk factors.

1 reference

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21 January 2018

A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers.

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-15-1008

21 January 2018

A stroma-related gene signature predicts resistance to neoadjuvant chemotherapy in breast cancer

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https://api.crossref.org/works/10.1186%2F1471-2164-15-1008

21 January 2018

mTOR inhibition reverses Akt-dependent prostate intraepithelial neoplasia through regulation of apoptotic and HIF-1-dependent pathways

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https://api.crossref.org/works/10.1186%2F1471-2164-15-1008

21 January 2018

Gene modules and response to neoadjuvant chemotherapy in breast cancer subtypes: a pooled analysis.

1 reference

https://api.crossref.org/works/10.1186%2F1471-2164-15-1008

21 January 2018

Biological Processes Associated with Breast Cancer Clinical Outcome Depend on the Molecular Subtypes

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https://api.crossref.org/works/10.1186%2F1471-2164-15-1008

21 January 2018

TAILORx: trial assigning individualized options for treatment (Rx)

1 reference

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10.1186/1471-2164-15-1008

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Europe PubMed Central

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5 August 2017

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