Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

12 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

SUBMITTER: Annuska Glas

PROVIDER: E-TABM-115 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Converting a breast cancer microarray signature into a high-throughput diagnostic test.

Glas Annuska M AM Floore Arno A Delahaye Leonie J M J LJ Witteveen Anke T AT Pover Rob C F RC Bakx Niels N Lahti-Domenici Jaana S T JS Bruinsma Tako J TJ Warmoes Marc O MO Bernards René R Wessels Lodewyk F A LF Van't Veer Laura J LJ

BMC genomics 20061030

<h4>Background</h4>A 70-gene tumor expression profile was established as a powerful predictor of disease outcome in young breast cancer patients. This profile, however, was generated on microarrays containing 25,000 60-mer oligonucleotides that are not designed for processing of many samples on a routine basis.<h4>Results</h4>To facilitate its use in a diagnostic setting, the 70-gene prognosis profile was translated into a customized microarray (MammaPrint) containing a reduced set of 1,900 prob ...[more]

PMID: 17074082

Similar Datasets

Transcription profiling of mouse ES cell embrioid bodies treated with retinoic acid

Project description:Neural induction of ES by Retinoic acid

2005-01-01 | E-MNIA-63 | biostudies-arrayexpress

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

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

Transcription profiling of mouse embryonic stem vs trophoblastic stem cells

Project description:We attempted to identify candidate genes that are expressed more highly in the ICM than in TE cells. Mouse ES cells are cultured from the ICM, whereas mouse TS cells are cultured from the TE. Although these cells have been cultured in vitro, they represent the in vitro equivalents of the ICM and TE. Therefore, genes which are expressed more highly in ES than TS in microarray studies were good candidates for genes predominantly expressed in the ICM in blastocysts.

2005-01-01 | E-MNIA-73 | biostudies-arrayexpress

Transcription profiling of parthenogenetic mouse embryos treated with cycloheximide or strontium chloride

Project description:gene expression pattern of parthenogenetic mouse embryos by cycloheximide or Sr2+.

2006-06-05 | E-MNIA-85 | 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

Transcription profiling of mouse embryonic stem cells with inducible Oct-3/4 or Tcl1 expression or Tcl1 knock out using siRNA

Project description:POU transcription factor Pou5f1 (Oct3/4) is required to maintain ES cells in an undifferentiated state. Here we show that global expression profiling of Oct3/4-manipulated ES cells delineates the downstream target genes of Oct3/4. Combined with data from genome-wide chromatin-immunoprecipitation assays, this analysis identifies not only primary downstream targets of Oct3/4, but also secondary or tertiary targets. Furthermore, the analysis also reveals that downstream target genes are regulated either positively or negatively by Oct3/4. Identification of a group of genes that show both activation and repression depending on Oct3/4 expression levels provides a possible mechanism for the requirement of appropriate Oct3/4 expression to maintain undifferentiated ES cells. As a proof-of-principle study, one of the downstream genes, Tcl1, has been analyzed in detail. We show that Oct3/4 binds to the promoter region of Tcl1 and activates its transcription. We also show that Tcl1 is involved in the regulation of proliferation, but not differentiation, in ES cells. These findings suggest that the global expression profiling of gene-manipulated ES cells can help to delineate the structure and dynamics of gene regulatory networks.

2006-11-30 | E-MNIA-61 | biostudies-arrayexpress

Transcription profiling of mouse ES cell neural induction (N2B27 monolayer cluture)

Project description:Neural induction of ES by N2B27 monolayer culture

2005-01-01 | E-MNIA-64 | biostudies-arrayexpress

Transcription profiling of human non-small cell lung cancer samples

Project description:Microarray gene expression analysis of genes that showed a gene copy number difference in non small cell lung cancer samples. Only data for a subset of the genes on the array chip are shown here.

2008-05-11 | E-TABM-270 | biostudies-arrayexpress

Identification of differentially expressed genes in human alveolar bone cells cultured on different titanium surfaces.

Project description:To evaluate mRNA expression profile (transcriptome), we identified mRNAs of osteoblastic cells from human alveolar crest culture in contact with different titanium surfaces: control (polished), nanotextured (polished titanium discs, etching at 25oC with 50% H2SO4conc and 50% H2O2aq) , nano+submicrotextured (polished titanium discs, etching at 50oC with 50% H2SO4conc and 50% H2O2aq) and rough microtexture (polished titanium discs, etching at 50oC with 100% H2O2aq). The osteoblastic cells were cultured in the alpha-minimum essential medium, supplemented with fetal bovine serum, gentamicin, fungizone, dexamethasone, ascorbic acid and β-glycerophosphate. The mRNA expression profiling was analyzed through hybridizations with whole-human genome Agilent microarray (4x44K format).

2014-11-14 | E-MTAB-3091 | 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