Integrated analysis of gene expression, CpG island methylation, and gene copy number in breast cancer cells by deep sequencing (Q28742371)

Krishna R Kalari

3

0 references

Zhifu Sun

Zhifu Sun

1

0 references

Edith A. Perez

12

Edith A Perez

0 references

author name string

Yan W Asmann

2

0 references

Jeanette E Eckel-Passow

5

0 references

Tiffany R Baker

6

0 references

Jennifer M Carr

7

0 references

Irina Khrebtukova

8

0 references

Shujun Luo

9

0 references

Lu Zhang

10

0 references

Gary P Schroth

11

0 references

E Aubrey Thompson

Creative Commons Attribution 4.0 International

13

0 references

language of work or name

English

0 references

publication date

25 February 2011

0 references

published in

PLOS One

0 references

volume

6

0 references

issue

2

0 references

page(s)

e17490

0 references

copyright license

start time

25 February 2011

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

limma

LIMMA

2 references

Europe PubMed Central

22 June 2022

https://europepmc.org/article/PMC/3045451

based on heuristic

inferred from PubMed Central ID database lookup

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

SQL

1 reference

Europe PubMed Central

26 June 2022

https://europepmc.org/article/PMC/PMC3045451

based on heuristic

inferred from PubMed Central ID database lookup

DESeq2

DESeq

1 reference

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

cites work

Copine-III interacts with ErbB2 and promotes tumor cell migration

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3045451

Fast and accurate short read alignment with Burrows-Wheeler transform

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3045451

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

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3045451

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3045451

Gene expression signature of estrogen receptor alpha status 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=3045451

Daxx-mediated transcriptional repression of MMP1 gene is reversed by SPOP

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3045451

Transcriptional coregulator SNURF (RNF4) possesses ubiquitin E3 ligase activity

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3045451

Statistical significance for genomewide studies

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3045451

Defining the galaxy of gene expression 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=3045451

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=3045451

Molecular portraits of human breast tumours

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3045451

The hereditary renal cell carcinoma 3;8 translocation fuses FHIT to a patched-related gene, TRC8

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3045451

CNV-seq, a new method to detect copy number variation using high-throughput sequencing

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3045451

Supervised risk predictor of breast cancer based on intrinsic subtypes

6 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3045451

A comparison of PAM50 intrinsic subtyping with immunohistochemistry and clinical prognostic factors in tamoxifen-treated 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=3045451

Ancestry-shift refinement mapping of the C6orf97-ESR1 breast cancer susceptibility locus

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3045451

Gene expression profile for predicting survival in advanced-stage serous ovarian cancer across two independent datasets

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3045451

LYN is a mediator of epithelial-mesenchymal transition and a target of dasatinib in breast cancer

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3045451

GATA3 in development and cancer differentiation: cells GATA have it!

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3045451

Oestrogen receptors and small nuclear ring finger protein 4 (RNF4) in malignant ovarian germ cell tumours

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3045451

Association between invasive ovarian cancer susceptibility and 11 best candidate SNPs from breast cancer genome-wide association study

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3045451

Genome-wide association study identifies a new breast cancer susceptibility locus at 6q25.1.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3045451

GATA-3 as a marker of hormone response in breast cancer.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3045451

Gene expression profiling identifies lobe-specific and common disruptions of multiple gene networks in testosterone-supported, 17beta-estradiol- or diethylstilbestrol-induced prostate dysplasia in Noble rats

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3045451

Cross-study analysis of gene expression data for intermediate neuroblastoma identifies two biological subtypes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3045451

Selective estrogen receptor modulators: discrimination of agonistic versus antagonistic activities by gene expression profiling in breast cancer cells

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3045451

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3045451

Methods for assessing reproducibility of clustering patterns observed in analyses of microarray data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3045451

Coregulator small nuclear RING finger protein (SNURF) enhances Sp1- and steroid receptor-mediated transcription by different mechanisms

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3045451

Estrogen and progesterone receptor status affect genome-wide DNA methylation profile in breast cancer

3 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0017490

Molecular characterization of breast cancer with high-resolution oligonucleotide comparative genomic hybridization array.

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0017490

A hedgehog-induced BTB protein modulates hedgehog signaling by degrading Ci/Gli transcription factor.

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0017490

Estrogen receptor status in breast cancer is associated with remarkably distinct gene expression patterns

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3045451

Predicting features of breast cancer with gene expression patterns

27 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21364760

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0017490

1 reference

2938324

ADS bibcode

2011PLoSO...617490S

0 references

2938324

1 reference

1 reference

1 reference