Whole transcriptome RNA-Seq analysis of breast cancer recurrence risk using formalin-fixed paraffin-embedded tumor tissue (Q28727086)

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Francois Collin

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Michael Crager

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Mei-Lan Liu

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Robert J Pelham

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Mylan Pho

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Andrew Dei Rossi

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Jennie Jeong

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Aaron Scott

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Ranjana Ambannavar

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Christina Zheng

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Raul Mena

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Jose Esteban

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James Stephans

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John Morlan

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Joffre Baker

Creative Commons Attribution 4.0 International

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language of work or name

English

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publication date

2012

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e40092

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start time

13 July 2012

1 reference

April 2022 Public Data File from Crossref

copyrighted

0 references

describes a project that uses

Cytoscape

object named as

Cytoscape

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

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17 March 2017

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Sequencing technologies - the next generation

17 March 2017

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Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

17 March 2017

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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

17 March 2017

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Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

17 March 2017

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MicroRNAs: target recognition and regulatory functions

17 March 2017

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RNA-Seq: a revolutionary tool for transcriptomics

17 March 2017

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Mapping and quantifying mammalian transcriptomes by RNA-Seq

17 March 2017

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Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs

17 March 2017

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Fewer Genes, More Noncoding RNA

17 March 2017

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Reactome: a knowledgebase of biological pathways

17 March 2017

1 reference

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

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396611

MicroRNAs: genomics, biogenesis, mechanism, and function

17 March 2017

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396611

17 March 2017

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0040092

Cytoscape: a software environment for integrated models of biomolecular interaction networks

21 January 2018

1 reference

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A gene-expression signature as a predictor of survival in breast cancer

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396611

Gene expression profiling predicts clinical outcome of breast cancer

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396611

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

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396611

Cluster analysis and display of genome-wide expression patterns

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396611

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396611

Cytoscape 2.8: new features for data integration and network visualization

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396611

lincRNAs act in the circuitry controlling pluripotency and differentiation

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396611

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

7 April 2017

1 reference

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RNA sequencing: advances, challenges and opportunities

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396611

Estrogen receptor (ESR1) mRNA expression and benefit from tamoxifen in the treatment and prevention of estrogen receptor-positive breast cancer

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396611

Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396611

Relevance of breast cancer hormone receptors and other factors to the efficacy of adjuvant tamoxifen: patient-level meta-analysis of randomised trials

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396611

Computational methods for transcriptome annotation and quantification using RNA-seq

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396611

Molecular classification of thyroid nodules using high-dimensionality genomic data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396611

Characterization of the RNA content of chromatin

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396611

Detection of splice junctions from paired-end RNA-seq data by SpliceMap.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396611

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396611

Clinical implications and longitudinal alteration of peripheral blood transcriptional signals indicative of future cardiac allograft rejection

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396611

Transcriptional signals of T-cell and corticosteroid-sensitive genes are associated with future acute cellular rejection in cardiac allografts

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396611

Multiplex PCR detection of GSTM1, GSTT1, and GSTP1 gene variants: simultaneously detecting GSTM1 and GSTT1 gene copy number and the allelic status of the GSTP1 Ile105Val genetic variant

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396611

A population-based study of tumor gene expression and risk of breast cancer death among lymph node-negative patients

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396611

Gene expression and benefit of chemotherapy in women with node-negative, estrogen receptor-positive breast cancer

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396611

Gene expression profiles in paraffin-embedded core biopsy tissue predict response to chemotherapy in women with locally advanced breast cancer

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396611

Measurement of gene expression in archival paraffin-embedded tissues: development and performance of a 92-gene reverse transcriptase-polymerase chain reaction assay

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396611

Unlocking the archive--gene expression in paraffin-embedded tissue

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396611

Quantitative mRNA expression analysis from formalin-fixed, paraffin-embedded tissues using 5' nuclease quantitative reverse transcription-polymerase chain reaction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396611

Effects of fixation on RNA extraction and amplification from laser capture microdissected tissue

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396611

A randomized clinical trial evaluating tamoxifen in the treatment of patients with node-negative breast cancer who have estrogen-receptor-positive tumors

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396611

Treatment of lymph-node-negative, oestrogen-receptor-positive breast cancer: long-term findings from National Surgical Adjuvant Breast and Bowel Project randomised clinical trials.

20 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0040092

Challenges translating breast cancer gene signatures into the clinic

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0040092

A direct approach to false discovery rates

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0040092

The Functional Genomics of Noncoding RNA

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0040092

Gene identification using true discovery rate degree of association sets and estimates corrected for regression to the mean.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3396611

Glutathione S-transferase T1 and M1 genotypes in normal mucosa, transitional mucosa and colorectal adenocarcinoma

27 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22808097

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Correlation of estrophilin content of primary mammary cancer to eventual endocrine treatment

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22808097