Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA321310 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:samples contain normal, Barrett and duodenum and adenocarcinoma BACKGROUND & AIMS: Barrett's esophagus is a precursor of esophageal adenocarcinoma. DNA microarrays that enable a genome-wide assessment of gene expression enhance the identification of specific genes as well as gene expression patterns that are expressed by Barrett's esophagus and adenocarcinoma compared with normal tissues. Barrett's esophagus length has also been identified as a risk factor for progression to adenocarcinoma, but whether there are intrinsic biological differences between short-segment and long-segment Barrett's esophagus can be explored with microarrays. METHODS: Gene expression profiles for endoscopically obtained biopsy specimens of Barrett's esophagus or esophageal adenocarcinoma and associated normal esophagus and duodenum were identified for 17 patients using DNA microarrays. Unsupervised and supervised approaches for data analysis defined similarities and differences between the tissues as well as correlations with clinical phenotypes. RESULTS: Each tissue displays a unique expression profile that distinguishes it from others. Barrett's esophagus and esophageal adenocarcinoma express a unique set of stromal genes that is distinct from normal tissues but similar to other cancers. Adenocarcinoma also showed lower and higher expression for many genes compared with Barrett's esophagus. No difference in gene expression was found between short-segment and long-segment Barrett's esophagus. CONCLUSIONS: The genome-wide assessment provided by current DNA microarrays reveals many candidate genes and patterns not previously identified. Stromal gene expression in Barrett's esophagus and adenocarcinoma is similar, indicating that these changes precede malignant transformation. A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied. Keywords: disease_state_design
2006-10-18 | GSE6059 | GEO
Project description:Barrett's esophagus transcriptome was analysed and compared with Barrett's esophagus primary cell culture and esophageal adenocarcinoma. Keywords: SAGE analysis to compare tissues Barrett's esophagus biopsy was taken from 1 male metaplastic Barrett's esophagus patient. Barrett's esophagus primary cell culture was cultures from a biopsy taken from a Barrett's esophagus patient and cultured for about 4 to 5 weeks. Esophageal adenocarcinoma was taken from a patient known to have cancer and previously Barrett's esophagus
2006-06-28 | E-GEOD-5155 | biostudies-arrayexpress
Project description:Methylation-based subtypes were identified in nondysplastic Barrett's Esophagus (BE) from BE-only patients (n=62) and Esophageal Adenocarcinoma (n=23) using RPMM-based clustering on methylation data at probes with the most variant Beta-values on the HM450 platform. Samples in these methylation-based subtypes were further identified in the TCGA EAC dataset, and subtypes were characterized using integrated analysis of methylation, sequencing, and expression data.
2019-01-01 | GSE81334 | GEO
Project description:Barrett's esophagus transcriptome was analysed and compared with Barrett's esophagus primary cell culture and esophageal adenocarcinoma. Keywords: SAGE analysis to compare tissues
2006-06-28 | GSE5155 | GEO
Project description:Barrett's esophagus is a metaplastic condition of the distal esophagus, characterized by the replacement of normal squamous epithelium by columnar epithelium. Patients with BE have an increased risk of developing esophageal adenocarcinoma. MicroRNAs have been implicated to be disease and tissue specific, however limited data of microRNA expression in the esophagus is available. Therefore we evaluated microRNA expression profiles of esophageal adenocarcinoma and compared these with Barrett's esophagus and normal squamous esophagus.
2012-03-15 | GSE29965 | GEO
Project description:miR-223 is step-wise increasingly up-regulated in the normal esophagus - Barrett's esophagus -esophageal adenocarcinoma carcinoma sequence. In this study, we aimed to determine the function of miR-223 in esophageal adenocarcinoma carcinogenesis.
2013-02-07 | GSE44120 | GEO
Project description:Dysplasia and early cancer are hard to detect in endoscopic biopsies and hence this study was carried out to evaluate the biomarker potential of DNA methylation to detect dyspasia and early cancer in Barrett's esophaghus patients. Bisulfite converted genomic DNA was hybridized onto Illumina 27k methylation arrays. 22 Barrett's esophagus (BE) and 2 Duodenum vs. 24 esophageal adenocarcinoma (EAC)
2013-01-28 | E-GEOD-32925 | biostudies-arrayexpress
Project description:The aim of this project is to identify circulatory diagnostic glycoprotein biomarkers for Barrett's esophagus (BE) and esophageal adenocarcinoma (EAC). Serum samples from healthy, BE and EAC patients were screened using LeMBA-LC-MS/MS-GlycoSelector pipeline as described in the manuscript.
2015-09-25 | PXD002442 | Pride
Project description:RNA-seq was performed on esophageal adenocarcinoma (EAC), Barrett's without dysplasia, Barrett's with low-grade dysplasia (LGD) and normal squamous esophagus tissue to find early alterations in the transcriptome level turning Barrett's dysplastic.
2017-07-23 | E-MTAB-4054 | biostudies-arrayexpress
Project description:To test the hypothesis that there is a specific miRNA expression signature which characterizes Barrett's esophagus development and progression, we performed miRNA microarray analysis comparing normal esophageal squamous epithelium with all the phenotypic lesions seen in the Barrett's carcinogenic process miRNA microarray analysis was performed in a series of 14 normal esophageal squamous epithelium samples, 14 Barrett's mucosa samples, 7 low-grade intra-epithelial neoplasia samples, 5 high-grade intra-epithelial neoplasia samples and 11 Barrett's adenocarcinoma samples
2010-01-29 | E-GEOD-20099 | biostudies-arrayexpress