(Q28244320)

object of statement has role

genomics

Medical Subject Headings

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A25043054

21 June 2025

20

David L Tabb

0 references

Sherri R Davies

Sherri R Davies

11

0 references

Daniel C. Liebler

Daniel C Liebler

23

0 references

Robbert J C Slebos

22

Robbert J C Slebos

0 references

Bing Zhang

1

Bing Zhang

0 references

author name string

Jing Wang

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A25043054

21 June 2025

Xiaojing Wang

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A25043054

21 June 2025

Jing Zhu

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A25043054

21 June 2025

Qi Liu

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A25043054

21 June 2025

Zhiao Shi

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A25043054

21 June 2025

Sangtae Kim

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A25043054

21 June 2025

Sean Wang

12

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A25043054

21 June 2025

Pei Wang

13

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A25043054

21 June 2025

Henry Rodriguez

16

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A25043054

21 June 2025

Matthew C. Chambers

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A25043054

21 June 2025

Lisa J. Zimmerman

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A25043054

21 June 2025

Kent F. Shaddox

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A25043054

21 June 2025

Christopher R. Kinsinger

14

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A25043054

21 June 2025

Robert C. Rivers

15

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A25043054

21 June 2025

R. Reid Townsend

17

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A25043054

21 June 2025

Matthew J. C. Ellis

18

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A25043054

21 June 2025

Steven A. Carr

19

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A25043054

21 June 2025

David L. Tabb

20

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A25043054

21 June 2025

Robert J. Coffey

21

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A25043054

21 June 2025

NCI CPTAC

24

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A25043054

21 June 2025

publication date

18 September 2014

0 references

20 July 2014

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A25043054

https://europepmc.org/articles/pmc4249766?pdf=render

21 June 2025

language of work or name

English

0 references

work available at URL

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A25043054

https://europepmc.org/articles/PMC4249766

21 June 2025

file format

HyperText Markup Language

online access status

open access

content deliverer

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A25043054

https://europepmc.org/articles/PMC4249766?pdf=render

21 June 2025

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A25043054

https://doi.org/10.1038/nature13438

21 June 2025

online access status

open access

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A25043054

http://www.nature.com/articles/nature13438.pdf

21 June 2025

1 reference

https://api.crossref.org/works/10.1038/NATURE13438

http://www.nature.com/articles/nature13438

21 June 2025

1 reference

https://api.crossref.org/works/10.1038/NATURE13438

21 June 2025

0 references

513

0 references

issue

7518

0 references

page(s)

382-7

0 references

cites work

Endocrine-therapy-resistant ESR1 variants revealed by genomic characterization of breast-cancer-derived xenografts

1 reference

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Integrated genomic characterization of endometrial carcinoma

20 March 2017

1 reference

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20 March 2017

Cancer genome landscapes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249766

Comprehensive molecular portraits of human breast tumours

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249766

Comprehensive genomic characterization of squamous cell lung cancers

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249766

Comprehensive molecular characterization of human colon and rectal cancer

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249766

Integrated genomic analyses of ovarian carcinoma

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249766

Genome remodelling in a basal-like breast cancer metastasis and xenograft

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249766

Transitions between epithelial and mesenchymal states: acquisition of malignant and stem cell traits

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249766

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249766

Anomalous features of EMT during keratinocyte transformation

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249766

WebGestalt: an integrated system for exploring gene sets in various biological contexts

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249766

Molecular portraits of human breast tumours

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249766

A model for random sampling and estimation of relative protein abundance in shotgun proteomics

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249766

Supervised risk predictor of breast cancer based on intrinsic subtypes

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249766

Regularized Multivariate Regression for Identifying Master Predictors with Application to Integrative Genomics Study of 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=4249766

customProDB: an R package to generate customized protein databases from RNA-Seq data for proteomics search

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249766

NetGestalt: integrating multidimensional omics data over biological networks

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249766

Identification and Selective Degradation of Neopeptide-Containing Truncated Mutant Proteins in the Tumors with High Microsatellite Instability

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249766

Poor-prognosis colon cancer is defined by a molecularly distinct subtype and develops from serrated precursor lesions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249766

A colorectal cancer classification system that associates cellular phenotype and responses to therapy

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249766

HNF4α: A New Biomarker in Colon Cancer?

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249766

Insights into the regulation of protein abundance from proteomic and transcriptomic analyses

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249766

Protein identification using customized protein sequence databases derived from RNA-Seq data

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249766

Genetic Variation Shapes Protein Networks Mainly through Non-transcriptional Mechanisms

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249766

Systematic investigation of genetic vulnerabilities across cancer cell lines reveals lineage-specific dependencies in ovarian cancer

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249766

Comparative analysis of proteome and transcriptome variation in mouse

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249766

EMT is the dominant program in human colon cancer

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249766

Global signatures of protein and mRNA expression levels

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249766

Correlations between RNA and protein expression profiles in 23 human cell lines

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249766

Biomarkers for epithelial-mesenchymal transitions

29 September 2017

1 reference

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Genetic basis of proteome variation in yeast

29 September 2017

1 reference

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Identification of TOMM34, which shows elevated expression in the majority of human colon cancers, as a novel drug target

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249766

Hepatocyte nuclear factor 4alpha is essential for embryonic development of the mouse colon

29 September 2017

1 reference

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Robustness, scalability, and integration of a wound-response gene expression signature in predicting breast cancer survival

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249766

Identification of genes involved in epithelial-mesenchymal transition and tumor progression

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249766

Activating SRC mutation in a subset of advanced human colon cancers

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4249766

System-wide molecular evidence for phenotypic buffering in Arabidopsis

29 September 2017

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

Automation of nanoscale microcapillary liquid chromatography-tandem mass spectrometry with a vented column

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

Supporting tool suite for production proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

A cross-platform toolkit for mass spectrometry and proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

Pepitome: evaluating improved spectral library search for identification complementarity and quality assessment

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

The generating function of CID, ETD, and CID/ETD pairs of tandem mass spectra: applications to database search

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

IDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

Improved LC-MS/MS spectral counting statistics by recovering low-scoring spectra matched to confidently identified peptide sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

Proteomic consequences of a single gene mutation in a colorectal cancer model

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

Detecting differential and correlated protein expression in label-free shotgun proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

Comparative shotgun proteomics using spectral count data and quasi-likelihood modeling.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-Seq gene expression data

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

Comparison of label-free methods for quantifying human proteins by shotgun proteomics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

Proteogenomic analysis reveals unanticipated adaptations of colorectal tumor cells to deficiencies in DNA mismatch repair.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

Proteomic analysis of oropharyngeal carcinomas reveals novel HPV-associated biological pathways

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

A comparison of normalization methods for high density oligonucleotide array data based on variance and bias

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

Integrative omics analysis reveals the importance and scope of translational repression in microRNA-mediated regulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

Targeted proteomic quantification on quadrupole-orbitrap mass spectrometer.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

Global quantification of mammalian gene expression control

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

Hepatocyte nuclear factor-4alpha promotes gut neoplasia in mice and protects against the production of reactive oxygen species

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

Inhibition of colorectal cancer by targeting hepatocyte nuclear factor-4alpha

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

Src tyrosine kinase phosphorylation of nuclear receptor HNF4α correlates with isoform-specific loss of HNF4α in human colon cancer

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

Silhouettes: A graphical aid to the interpretation and validation of cluster analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

Diagnosis of multiple cancer types by shrunken centroids of gene expression

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

GO-function: deriving biologically relevant functions from statistically significant functions

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

Correlation of Relative Abundance Ratios Derived from Peptide Ion Chromatograms and Spectrum Counting for Quantitative Proteomic Analysis Using Stable Isotope Labeling

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

Statistical Analysis of Membrane Proteome Expression Changes inSaccharomycescerevisiae

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

Molecular Genetics of Colorectal Cancer

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25043054

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Regulation of the tumor suppressor homeogene Cdx2 by HNF4α in intestinal cancer

1 reference

https://api.crossref.org/works/10.1038%2FNATURE13438

inferred from DOI database lookup

7 January 2021

based on heuristic

12

5

1512

R de Sousa Abreu

2009

1 reference

https://api.crossref.org/works/10.1038/NATURE13438

21 June 2025

Identifiers

DOI

10.1038/NATURE13438

1 reference

Dimensions Publication ID

1013665739

0 references

1 reference

1 reference

1 reference