Proteogenomic characterization of human colon and rectal cancer (Q28244320)

Sherri R Davies

11

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Daniel C. Liebler

Daniel C Liebler

23

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Robbert J C Slebos

22

Robbert J C Slebos

0 references

Bing Zhang

1

Bing Zhang

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author name string

Jing Wang

2

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Xiaojing Wang

3

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Jing Zhu

4

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Qi Liu

5

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Zhiao Shi

6

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Matthew C Chambers

7

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Lisa J Zimmerman

8

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Kent F Shaddox

9

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Sangtae Kim

10

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Sean Wang

12

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Pei Wang

13

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Christopher R Kinsinger

14

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Robert C Rivers

15

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Henry Rodriguez

16

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R Reid Townsend

17

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Matthew J C Ellis

18

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Steven A Carr

19

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Robert J Coffey

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

21

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language of work or name

English

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publication date

18 September 2014

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published in

Nature

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volume

513

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page(s)

382-7

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issue

7518

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cites work

1 reference

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

Integrated genomic characterization of endometrial 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

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

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

Genetic basis of proteome variation in yeast

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 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

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

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

Identifiers

DOI

10.1038/NATURE13438

1 reference

Dimensions Publication ID

1620696

1013665739

0 references

1620696

1 reference

1 reference

1 reference