Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

11 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Breast tumor gene expression profiling for assessment of sufficient tumor cells for microarray diagnostic

ABSTRACT: Gene expression profiling of breast cancer primary tumor was performed to identify gene expression that is related to the presence of sufficient tumor cells. These gene profile can be used for identification of tumor samples that are eligible for microarray diagnostics. A cohort of 403 early-stage primary breast cancer tumors was analyzed against a breast cancer reference pool

ORGANISM(S): Homo sapiens

SUBMITTER: Annuska Glas

PROVIDER: E-GEOD-16201 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

A gene expression profile for detection of sufficient tumour cells in breast tumour tissue: microarray diagnosis eligibility.

Roepman Paul P Schuurman Arenda A Delahaye Leonie J M J LJ Witteveen Anke T AT Floore Arno N AN Glas Annuska M AM

BMC medical genomics 20090812

<h4>Background</h4>Microarray diagnostics of tumour samples is based on measurement of prognostic and/or predictive gene expression profiles. Typically, diagnostic profiles have been developed using bulk tumour samples with a sufficient amount of tumour cells (usually >50%). Consequentially, a diagnostic results depends on the minimal percentage of tumour cells within a sample. Currently, tumour cell percentage is assessed by conventional histopathological review. However, even for experienced p ...[more]

PMID: 19674463

Similar Datasets

A gene expression profile that predicts circulating tumor cell presence in breast cancer patients

Project description:Development of a primary tumor gene expression profile that can predict the presence of circulating tumor cells in the blood of breast cancer patients. The detection of circulating tumor cells (CTCs) in the peripheral blood and microarray gene expression profiling of the primary tumor are two promising new technologies able to provide valuable prognostic data for patients with breast cancer. In the current study, we aimed to develop a novel profile which provided independent prognostic data by building a signature predictive of CTC status rather than outcome. Seventy-two primary breast cancer tumor have been analyzed against a breast cancer reference pool.

2012-04-11 | E-GEOD-31364 | biostudies-arrayexpress

Transcription profiling of human node-negative breast cancer patients to validate a 70-gene prognostic signature on a high-throughput microarray

Project description:A 70-gene signature has been shown to be a powerful predictor of disease outcome in young breast cancer patients. The microarrays were not designed for high throughput processing. To facilitate the use in a diagnostic setting, the profile was translated into a customized microarray containing a reduced set of 1,900 probes.

2007-02-23 | E-TABM-115 | biostudies-arrayexpress

Expression profiling of response to first-line aromatase inhibitor therapy

Project description:Fresh-frozen primary cancer specimens of 107 breast cancer patients whose metastases were treated with first-line aromatase inhibitors were evaluated for their whole genome mRNA expression profiles. Primary breast tumors (107) were analyzed against a common breast cancer reference pool (BRP).

2013-12-05 | E-GEOD-41994 | biostudies-arrayexpress

Full genome expression profiling of primary colorectal cancer (CRC)

Project description:Fresh-frozen primary tumor samples from CRC patients were analyzed from their gene expression. Full genome unsupervised clustering identified three intrinsic subtypes that are associated with tumor and clinical characteristics. Primary CRC samples (188) were hybridzed against a common colon cancer reference pool (CRP).

2013-07-23 | E-GEOD-42284 | biostudies-arrayexpress

Uncovering tumor-stroma inter-relationships using quantitative MALDI-Mass spectrometry imaging

Project description:To facilitate analysis of protein expression changes in in situ tumors and stroma, we took advantage of a mouse model that permits conditional activation of the Ser-Thr kinase ROCK within mammary tumor cells. In this study, we undertook MALDI-MSI analysis of tissue samples derived from our conditional ROCK mammary tumor model, to quantify in an unbiased manner, the proteomic changes occurring during the progression of mammary cancers in their specific spatial contexts.

2020-09-07 | PXD019255 | Pride

Transcriptional profiling of human breast cancer cell lines.

Project description:In an experimental model of tumor dormancy, heat shock protein 27 (HSP27) was up-regulated in angiogenic human breast cancer cells when compared with non-angiogenic cells. Stable down-regulation of HSP27 in angiogenic tumor cells was followed by long-term tumor dormancy in vivo and associated with reduced intra-tumoral endothelial cell proliferation, decreased secretion of VEGF and bFGF from tumor cells, and increased expression of thrombospondin-1. Phosphorylation of the transcription factor STAT3 and nuclear expression of NFÎºB were reduced following suppression of HSP27. In contrast, tumor cell proliferation and apoptosis were not affected. By clinical validation, high HSP27 expression was associated with markers of aggressive tumors and decreased survival in breast cancer and melanoma patients. Our present findings suggest a link between HSP27 and dormancy through tumor-vascular interactions. Targeting HSP27, a multifunctional cytoprotective protein, might offer a novel strategy in cancer treatment.

2010-02-28 | E-TABM-883 | biostudies-arrayexpress

Quantitative Expression Profiling of RNA from Formalin-Fixed, Paraffin-Embedded (FFPE)and Fresh Frozen (FF) Breast Cancer samples

Project description:Unluckily, FFPE archival methods lead to partial RNA degradation, limiting the amount of derivable information. This study aims to evaluate if the DASL gene expression assay, designed to generate reproducible data from degraded RNAs, is a reliable method to apply on RNA from FFPE tissues. In order to do that, we analyzed 20 FFPE breast cancer samples and 20 FF (Fresh Frozen) matched samples with the Illumina Whole Genome DASL platform for a genome-wide expression profiling.

2011-09-05 | E-TABM-1081 | biostudies-arrayexpress

Microdissected tumor epithelium and tumor stroma from patients with breast cancer

Project description:Stratification of breast cancers into subtypes are generally based on immune assays on tumor cells and/or mRNA expression of tumor cell enriched tissues. Here, we have laser microdissected tumor epithelium and tumor stroma from 24 breast cancer biopsies (12 luminal-like and 12 basal-like). We hypothesized that the stromal proteome would separate patients with breast into groups independently of the traditional epithelial based subtypes.

2023-06-23 | PXD027012 | Pride

Transcription profiling of human breast tissue tumors vs. normal tissue

Project description:bulk breast tumor RNA from patient; Abstract: Sporadic basal-like cancers (BLC) are a distinct class of human breast cancers that are phenotypically similar to BRCA1-associated cancers. Like BRCA1-deficient tumors, most BLC lack markers of a normal inactive X chromosome (Xi). Duplication of the active X chromosome and loss of Xi characterized almost half of BLC cases tested. Others contained biparental but nonheterochromatinized X chromosomes or gains of X chromosomal DNA. These abnormalities did not lead to a global increase in X chromosome transcription but were associated with overexpression of a small subset of X chromosomal genes. Other, equally aneuploid, but non-BLC rarely displayed these X chromosome abnormalities. These results suggest that X chromosome abnormalities contribute to the pathogenesis of BLC, both inherited and sporadic. total 62 sample incudes 43 tumor, 7 normal breast and 12 normal organelle Experiment Overall Design: compare expression of tumor to normal breast tissue

2008-06-16 | E-GEOD-7904 | biostudies-arrayexpress

Transcription profiling of rat DMBA induced mammary adeno carcinoma

Project description:Tumor hypoxia is relevant for tumor growth, metabolism and epithelial-to-mesenchymal transition (EMT). We report that hyperbaric oxygen (HBO) treatment induced mesenchymal-to-epithelial transition (MET) in a dimetyl-Î±-benzantracene induced mammary rat adenocarcinoma model, and the MET was associated with extensive coordinated gene expression changes and less aggressive tumors. One group of tumor bearing rats was exposed to HBO (2 bar, pO2 = 2 bar, 4 exposures Ã 90 minutes), whereas the control group was housed under normal atmosphere (1 bar, pO2 = 0.2 bar). Treatment effects were determined by assessment of tumor growth, tumor vascularisation, tumor cell proliferation, cell death, collagen fibrils and gene expression profile. Tumor growth was significantly reduced (~16%) after HBO treatment compared to day 1 levels, whereas control tumors increased almost 100 % in volume. Significant decreases in tumor cell proliferation, tumor blood vessels and collagen fibrils, together with an increase in cell death, are consistent with tumor growth reduction and tumor stroma influence after hyperoxic treatment. Gene expression profiling showed that HBO induced MET with coordinated expression of gene modules involved in cell junctions and attachments together with a shift towards non-tumorigenic metabolism. This leads to more differentiated and less aggressive tumors, and indicates that oxygen per se might be an important factor in the â??switchesâ?? of EMT and MET in vivo. HBO treatment also attenuated tumor growth and changed tumor stroma, by targeting the vascular system, having anti-proliferative and pro-apoptotic effects.

2009-06-22 | E-TABM-718 | biostudies-arrayexpress

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