Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

2 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Integrated proteomic and N-glycoproteomic analyses of human breast cancer

ABSTRACT: In the present study, we systematically profiled proteomes and N-glycoproteomes of cancerous, paracancerous, and distal noncancerous tissues from patients with breast cancer by DIA.

ORGANISM(S): Homo Sapiens

SUBMITTER: Yaoyang Zhang

PROVIDER: PXD017358 | iProX | Thu Apr 30 00:00:00 BST 2020

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Publications

Integrated Proteomic and N-Glycoproteomic Analyses of Human Breast Cancer.

Wang Zhiyuan Z Liu Hua H Yan Yu Y Yang Xiangyun X Zhang Yaoyang Y Wu Linshi L

Journal of proteome research 20200616 8

Breast cancer is one of the most common cancers in women worldwide. In the past decades, many advances have been made in understanding and treating breast cancer. However, due to the highly heterogeneous nature of this disease, a precise characterization of breast cancer on the molecular level is of great importance but not yet readily available. In the present study, we systematically profiled proteomes and N-glycoproteomes of cancerous, paracancerous, and distal noncancerous tissues from patie ...[more]

PMID: 32543193

Similar Datasets

Analysis of Human Breast Tumors by Integrated Proteotranscriptomics

Project description:We generated large-scale proteome data for 65 human breast tumors and 53 paired adjacent non-cancerous tissue and performed an integrated proteotranscriptomic characterization. To our best knowledge, the study is one of the largest quantitative proteomic study of human breast tissues, including the analysis of 118 tissue samples from 65 patients with long-term survival outcomes. Our data show that protein expression describes a tumor biology that is only partly captured by the transcriptome, with mRNA abundance incompletely predicting protein abundance in tumors, and even less so in non-cancerous tissue. Furthermore, the tumor proteome described disease pathways and subgroups that were only partially captured by the tumor transcriptome.

2018-12-04 | PXD005692 | Pride

Integrated Proteomic and Glycoproteomic Analyses of Prostate Cancer Cells Reveal Glycoprotein Alteration in Protein Abundance and Glycosylation.

Project description: Not available

| S-EPMC4597149 | biostudies-literature

Integrated analyses identify phenotype specific BMP4 signaling in breast cancer [RNA-seq]

Project description:Bone morphogenetic protein 4 (BMP4) plays an important role in cancer pathogenesis. In breast cancer, it reduces proliferation and increases migration in a cell line-dependent manner. To characterize the transcriptional mediators of these phenotypes, we performed RNA-seq and DNase-seq analyses after BMP4 treatment in MDA-MB-231 and T-47D breast cancer cells that respond to BMP4 with enhanced migration and decreased cell growth, respectively.

2016-12-12 | GSE84577 | GEO

Integrated analyses identify phenotype specific BMP4 signaling in breast cancer [Dnase-seq]

2016-12-12 | GSE84578 | GEO

The protein interaction landscape of breast cancer

Project description:Cancers have been associated with diverse sets of genomic alterations, many of which are rare with uncertain significance. To understand the cellular mechanisms impacted by such alterations in breast invasive carcinoma, we have applied affinity-purification mass spectrometry to delineate comprehensive biophysical interaction networks for 40 frequently altered breast cancer proteins. These networks interconnect and enrich for common and rare cancer mutations; they are also substantially re-wired by mutations, including in TP53 and PIK3CA, and across cancerous and non-cancerous cell contexts. Our analysis identifies a novel AKT-interacting protein, S100A3, which we find activates AKT signaling and is predictive of clinical response to AKT inhibitors. Similarly, UBE2N emerges as a BRCA1 interactor predictive of clinical response to inhibition of PARP. Finally, we show that Spinophilin interacts with and dephosphorylates BRCA1 to promote DNA double strand break repair. Thus, cancer protein interaction landscapes provide a framework for recognizing oncogenic drivers and drug vulnerabilities.

2021-11-02 | PXD019639 | Pride

Integrated analyses identify phenotype specific BMP4 signaling in breast cancer

Project description:Integrated analyses identify phenotype specific BMP4 signaling in breast cancer

| PRJNA329667 | ENA

Breast cancer risk-associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression

Project description:Genome-wide association studies (GWASs) have identified thousands of single nucleotide polymorphisms (SNPs) associated with human traits and diseases. But because the vast majority of these SNPs are located in the noncoding regions of the genome their risk promoting mechanisms are elusive. Employing a new methodology combining cistromics, epigenomics and genotype imputation we annotate the noncoding regions of the genome in breast cancer cells and systematically identify the functional nature of SNPs associated with breast cancer risk. Our results demonstrate that breast cancer risk-associated SNPs are enriched in the cistromes of FOXA1 and ESR1 and the epigenome of H3K4me1 in a cancer and cell-type-specific manner. Furthermore, the majority of these risk-associated SNPs modulate the affinity of chromatin for FOXA1 at distal regulatory elements, which results in allele-specific gene expression, exemplified by the effect of the rs4784227 SNP on the TOX3 gene found within the 16q12.1 risk locus. Examination of histone modification H3K4me2 in untreated and E2 treated cells

2012-08-17 | E-GEOD-31151 | biostudies-arrayexpress

Methylation profiling of normal and cancerous human breast samples

Project description:To assess changes in DNA methylation state associated with breast cancer we analyzed DNA from normal and cancerous breast specimens on CpG islands microarray using methylation-sensitive enzyme McrBC for target preparation. Cy3 was used for McrBC cut sample, Cy5 was used for reference Mock sample.

2006-11-03 | E-MEXP-881 | biostudies-arrayexpress

Breast cancer subtype dictates DNA methylation and ALDH1A3-mediated expression of tumor suppressor RARRES1

Project description:Genome wide DNA methylation profiling of cancerous and normal breast cell lines, with and without decitabine. The Illumina HumanMethylation450 beadchip array was used.

2016-06-06 | GSE78875 | GEO

Comparative Membrane Proteomics Analyses of Breast Cancer Cell Lines to Understand the Molecular Mechanism of Breast Cancer Brain Metastasis

Project description:Breast cancer is the leading type of cancer in women. Breast cancer brain metastasis is considered as an essential issue in breast cancer patients. Membrane proteins play important roles in breast cancer brain metastasis that contributes to the cell adhesion and penetration of blood-brain barrier. To achieve a deeper insight of the mechanism of breast cancer brain metastasis, liquid chromatography tandem mass spectrometry (LC-MS/MS) was performed to analyze the enriched membrane proteomes from six different breast cancer cell lines. Quantitative proteomic data of all cell lines were compared with MDA-MB-231BR which has the specific brain metastasis capacity. 1239 proteins were identified and 990 were quantified with more than 70% of membrane proteins in all cell lines. Each cell line can be separated apart from others in PCA. Ingenuity pathway analysis (IPA) supported the high brain metastatic ability of 231BR and suggested importance of the up-regulation of integrin proteins and down-regulation of EPHA in brain metastasis. 28 proteins were observed unique expression alteration in 231BR. The up-regulation of NPM1, hnRNP Q, hnRNP K and eIF3l and the down-regulation of TUBB4B and TUBB were observed to be associated with the brain metastasis cell line and may contributes to the breast cancer brain metastasis.

2017-05-23 | PXD005719 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data