Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Differential protein expression between ESCC and normal tissues

ABSTRACT: To understand the difference of protein expression between paired esophageal squamous cell carcinoma (ESCC) and adjacent normal tissues, we collected 10 paired ESCC and normal tissues from surgical resected specimems for high-throughput proteomic experiments. From comparative analysis, the dysregulated signaling pathways in ESCC could be uncovered.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Esophageal Squamous Epithelium

DISEASE(S): Esophageal Cancer

SUBMITTER: Wei Wu

LAB HEAD: Wei Wu

PROVIDER: PXD019834 | Pride | 2020-08-11

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	1_1.wiff	Wiff
	1_10.wiff	Wiff
	1_2.wiff	Wiff
	1_3.wiff	Wiff
	1_4.wiff	Wiff

Items per page:

1 - 5 of 36

Publications

Multi-faceted epigenetic dysregulation of gene expression promotes esophageal squamous cell carcinoma.

Cao Wei W Lee Hayan H Wu Wei W Zaman Aubhishek A McCorkle Sean S Yan Ming M Chen Justin J Xing Qinghe Q Sinnott-Armstrong Nasa N Xu Hongen H Sailani M Reza MR Tang Wenxue W Cui Yuanbo Y Liu Jia J Guan Hongyan H Lv Pengju P Sun Xiaoyan X Sun Lei L Han Pengli P Lou Yanan Y Chang Jing J Wang Jinwu J Gao Yuchi Y Guo Jiancheng J Schenk Gundolf G Shain Alan Hunter AH Biddle Fred G FG Collisson Eric E Snyder Michael M Bivona Trever G TG

Nature communications 20200722 1

Epigenetic landscapes can shape physiologic and disease phenotypes. We used integrative, high resolution multi-omics methods to delineate the methylome landscape and characterize the oncogenic drivers of esophageal squamous cell carcinoma (ESCC). We found 98% of CpGs are hypomethylated across the ESCC genome. Hypo-methylated regions are enriched in areas with heterochromatin binding markers (H3K9me3, H3K27me3), while hyper-methylated regions are enriched in polycomb repressive complex (EZH2/SUZ1 ...[more]

PMID: 32699215

Similar Datasets

Expression data from esophageal squamous cell carcinoma (ESCC)

Project description:We used microarrays to determine global gene expression in primary tumor tissues (ESCC) and matched normal tissues (adjacent normal esophageal mucosa) Paired primary ESCC tumor and normal tissues were compared (n=5).

2009-09-01 | E-GEOD-17351 | biostudies-arrayexpress

Integrative genomics analysis of genes with biallelic loss and its relation to the expression of mRNA and micro-RNA in esophageal squamous cell carcinoma

Project description:Genomic instability plays an important role in human cancers. We previously characterized genomic instability in esophageal squamous cell carcinomas (ESCC) in terms of loss of heterozygosity (LOH) and copy number (CN) changes in tumors. In the current study we focus on biallelic loss and its relation to expression of mRNA and miRNA in ESCC using results from 500K SNP, mRNA, and miRNA arrays in 30 cases from a high-risk region of China. 30 matched tumors and normal tissue

2016-02-29 | E-GEOD-66274 | biostudies-arrayexpress

Gene Expression of Malignant Pleural Mesothelioma Tumor and paired Normal Lung tissue

Project description:In order to discover critical pathways /networks or therapeutic targets in pleural mesothelioma we profiled 55 tumors along with paired normal tissue (for 41 tumors) using Affymetrix U133 plus 2.0 chips RNA isolated from frozen resected tumor and normal tissues was hybridized to Affymetrix U133 plus 2.0 chips to discover genes upregulated/downregulated in mesothelioma tumors compared to paired normal non-tumor adjacent tissue as well as find differences between the different tumors

2014-08-31 | E-GEOD-51024 | biostudies-arrayexpress

Expression data from gastroesphageal cancers and adjascent normal tissue

Project description:The primary objective of this study was to determine the effectiveness of bortezomib alone or in combination with irinotecan in patients with advanced gastric and gastroesphageal cancer. A secondary objecitve was to determine whether treatment was associated with changes in gene expression in the tumor and normal adjascent tissue. Tumor biopsies and biopsies of normal adjascent tissue were obtained before therapy and 24 hours after therapy. Differences in gene expression were evaluated between tumor and normal tissue (N=8 patients), and between post-treatment and pretreatment specimens for bortezomib alone (N=2 patients) and bortezomib plus irinotecan (N=10 patients).

2013-11-07 | E-GEOD-52138 | biostudies-arrayexpress

Methylation in breast cancer vs. normal tissue

Project description:We applied a combination of Methyl-CpG Immunoprecipitation (MCIp) and Human CpG Island microarrays to identify aberrant DNA methylation in eight low-grade breast invasive carcinomas and two pre-invasive breast tumors against ten normal breast tissues. 10 breast tumor samples (8 invasive, 2 pre-invasive) and 10 normal breast tissues, paired randomly (except Array 10: matched pair)

2012-09-14 | E-GEOD-35263 | biostudies-arrayexpress

The dataset to discover ESCC related proteins

Project description:To discover ESCC related proteins, we used SWATH to quantify the protein abundance between ESCC and adjacent tissues. Briefly, we pooled 10 ESCCtissues and their corresponding adjacent tissues for SWATH acquisition with three replicates.Three DDA repeats were also acquired with the pooled 10-paired ESCC tissue.The trypsin digested peptide mixture was analyzed by AB SCIEX 5600 (AB SCIEX).The database searching procedure was achieved using ProteinPilot v4.5 (AB Sciex). The database is IPI_homo_sapiens_V3.87.

2015-09-22 | PXD001764 | Pride

Affymetrix SNP array data for soft tissue sarcoma samples

Project description:Soft tissue sarcomas are aggressive mesenchymal cancers that affect more than 10,600 new patients per year in the US, about 40% of whom will die of their disease. Soft tissue sarcomas exhibit remarkable histologic diversity, with more than 50 recognized subtypes, but our knowledge of their genomic alterations is limited. Here we describe the results of an integrative analysis of DNA sequence, copy number, and mRNA expression in 207 samples encompassing seven major subtypes. Genes mutated in more than 5% of samples within a subtype were KIT (in gastrointestinal stromal cell tumors, or GISTs), TP53 (pleomorphic liposarcomas), PIK3CA (myxoid/round-cell liposarcoma), and NF1 (both myxofibrosarcoma and pleomorphic liposarcoma). We show evidence that PIK3CA mutations, found in 18% of myxoid/round-cell liposarcomas, activate AKT in vivo and are associated with poor outcomes. Point mutations in the tumor suppressor gene NF1 were discovered in both myxofibrosarcomas and pleomorphic liposarcomas, while genomic deletions were observed in all subtypes at varying frequencies. Finally, we found that short hairpin RNA-based knockdown of a subset of genes that are amplified in dedifferentiated liposarcoma, including CDK4 and YEATS4, decreased cell proliferation. Our study yields the most detailed map of molecular alterations across diverse sarcoma subtypes to date and provides potential subtype-specific targets for therapy. Human soft tissue sarcoma samples and their matched normal DNA were profiled on Affymetrix 250K SNP (Sty) arrays per manufacturer's instructions

2010-07-05 | E-GEOD-21123 | biostudies-arrayexpress

A novel lncRNA, LUADT1 promotes lung adenocarcinoma proliferation by epigenetic suppression of p27

Project description:Long noncoding RNAs (lncRNAs) are known to regulate the development and progression of various cancers, however, few lncRNAs have been well characterized in lung adenocarcinoma (LUAD). Understanding the expression profile of lncRNAs and protein-coding genes is critical to develop new diagnosis and treatment strategies for LUAD and improving the prognosis of diagnosed patients. Five female LUAD patients with no smoking history were selected to profile lncRNA and protein-coding gene expression with microarrays. Paired tumor tissues and adjacent nontumor tissues were collected and confirmed by pathologists.

2015-03-10 | E-GEOD-66654 | biostudies-arrayexpress

Expression profiles and initial confirmation of long non-coding RNAs in Chinese patients with pulmonary adenocarcinoma

Project description:There are significant differences in the lncRNA expression profiles in Chinese patients with pulmonary adenocarcinoma. LncRNAs such as AK124939 may be anti-cancer factors related to the progress of pulmonary adenocarcinoma. RNA extracted from three paired pulmonary adenocarcinoma tissue and adjacent normal lung tissue specimens was used to synthesize double-stranded complementary DNA (cDNA) after labeling and hybridization. The cDNA was labeled and hybridized to the lncRNA expression microarray, and array data were analyzed for hierarchical clustering. Gene coexpression networks were constructed to identify interactions among genes. To validate the microarray findings, we measured the relative expression levels of four random differentially expressed lncRNAs in the same tissue used for microarray using real-time quantitative polymerase chain reaction (qRT-PCR). The expression level of one lncRNA AK124939, in the paired pulmonary adenocarcinoma/adjacent normal lung tissue of another 30 patients was measured using qRT-PCR. The experimental data were further analyzed and compared with clinical features.

2014-04-17 | E-GEOD-56850 | biostudies-arrayexpress

DNA methylation profiling in colon cancer

Project description:Profiling of CpG island methylation in 19 primary colon cancer and paired normal samples Agilent 244k CpG island microarray

2013-01-22 | E-GEOD-39334 | biostudies-arrayexpress