Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

30 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Candidate luminal B breast cancer genes identified by genome, gene expression and DNA methylation profiling

ABSTRACT: To better understand Luminal B subtype we studied in 188 breast cancers of various molecular subtypes, DNA copy number aberrations (CNAs), DNA promoter methylation and gene expression profiles. Please note mRNA expression data already submitted for study: E-GEOD-21653.

ORGANISM(S): Homo sapiens

SUBMITTER: Pascal Finetti

PROVIDER: E-MTAB-1861 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

breast cancer cell lines ALDH+/-

Project description:Self-renewal and differentiation are two epigenetic programs that regulate pluripotency of stem cells. During oncogenesis, dysregulation of these two programs leads to the development of cancer stem cells (CSCs). Here, we used a pan genomic promoter microarray to determine the DNA methylation portrait of breast cancer stem cells (bCSC) compared to non-bCSC

2015-01-01 | E-MTAB-2236 | biostudies-arrayexpress

Genome profiling of pancreatic adenocarcinoma

Project description:Pancreatic adenocarcinoma is one of the most aggressive human cancers and displays many different chromosomal abnormalities and mutations. By using 244K high-resolution array-comparative genomic hybridization (aCGH) we studied the genome alterations of 39 fine-needle aspirations from pancreatic adenocarcinoma and 9 human adenocarcinoma pancreatic cell lines.

2011-12-31 | E-MTAB-570 | biostudies-arrayexpress

Gene expression profiling in myeloproliferative neoplasms

Project description:Gene expression profiles were established for 50 MPNs samples. RNA extracted from 2 healthy people was used as control. All MPNs were screened for JAK2V617F mutation as part of routine diagnostic practice.

2011-12-31 | E-MTAB-510 | biostudies-arrayexpress

Inflammatory Breast Cancer

Project description:Gene expression profiles were established for Inflammatory breast cancer samples from patients treated at the Institut Paoli-Calmettes.

2014-01-13 | E-MTAB-1547 | biostudies-arrayexpress

Gene expression profiling of solitary fibrous tumors

Project description:Sixteen pre-treatment samples of pathologically confirmed solitary fibrous tumors (SFT) were available for RNA profiling. They were collected from 16 patients who underwent initial surgery and/or diagnostic biopsy. Samples were macrodissected by pathologists, and frozen within 30 min of removal in liquid nitrogen in our biobank (Biobank authorization number 2008/70, APHM). All profiled specimens contained more than 70% tumor cells. Each patient gave written informed consent for molecular analysis, and the study was approved by our institutional ethics committee. Total RNA was extracted from frozen samples by using the All-In-One Norgen Biotek kit (Thorold, Canada) and integrity was controlled by Agilent analysis (Bioanalyzer, Palo Alto, CA). Gene expression profiling was done with Affymetrix U133 Plus 2.0 human oligonucleotide microarrays with labeling kit and protocol from manufacturer.

2013-11-12 | E-MTAB-1361 | biostudies-arrayexpress

Gene expressionprofiling of breast cell lines

Project description:We performed gene expression profiling of 31 breast cell lines (BCL) using whole-genome DNA microarrays (Affymetrix U133+2.0) to assessed a better molecular characterization of breast cell lines in order to help discover of new markers to apply to tumour samples.

2013-06-10 | E-MTAB-1693 | biostudies-arrayexpress

siRNA profiling of human cancer cell line MDA-MB-231 knocked down for CD146 mRNA

Project description:Metastasis is a complex process involving loss of adhesion, migration, invasion and proliferation of cancer cells. Cell adhesion molecules play a pivotal role in this phenomenon by regulating cell-cell and cell-matrix interactions. CD146 (MCAM) is associated with advanced tumor stage in melanoma, prostate and ovarian cancers. For this study, the MDA-MB-231 cell line was used as a prototypic mesenchymal and invasive cell line, spontaneously expressing high levels of CD146. Using whole-genome DNA microarrays, we investigated genes for which expression was modified by CD146 down-regulation, obtained by siRNA or shRNA technology Experiment Overall Design: Expression profiles of two cell lines transfected by two differents ShRNA directed against CD146 were compared with expression profiles of 3 control cell lines (i.e. native cell line, empty plasmid and shRNA directed against GFP)

2008-10-21 | E-GEOD-11951 | biostudies-arrayexpress

Pregnane X-receptor (PXR/NR1I2) activity is a hallmark of cancer stem cells and drives post-treatment tumor recurrence in colon cancer

Project description:Post-treatment recurrence remains a major clinical challenge in colorectal cancer (CRC), and increasing evidence suggests that Cancer Stem Cells (CSCs) may mediate this process due to their enhanced resistance to conventional therapeutics. We hypothesized that the Pregnane-X receptor (PXR) may drive the chemoresistance of colorectal CSCs.. shRNA-mediated PXR down-regulation was used to analyze the role of PXR on self-renewal in the colorectal cancer cell Line LS174T. Expression and activity of PXR were quantified under conditions that promote Cancer Stem Cells (CSCs) enrichment. Conversely, CSC characterization was performed in cells enriched along their PXR activity level.

2016-08-01 | E-MTAB-3471 | biostudies-arrayexpress

Progastrin is essential for the survival and self-renewal of tumor-initiating cells in colorectal cancer

Project description:Using established human CRC cell lines, we showed that progastrin expression were enriched under conditions that promote tumor-initiating cells (TIC) self-renewal.

2016-06-29 | E-MTAB-3215 | biostudies-arrayexpress

The hijack of a cellular failsafe program at the initiation of colorectal cancers.

Project description:The aim of this study was to set up an in vitro model to highlight yet-unidentified mechanisms facilitating the escape of human colonic epithelial cells from chronic inflammation-induced senescence, and to define whether these mechanisms afford cells a resistance to oxidative stress thereby contributing to tumor initiation. By driving a specific genetic program (termed ALEP), as observed in ulcerative colitis and Crohn’s disease patients, transient expression of ZEB transcription factors buffers ROS deleterious effects and maintains intestinal stem cell (ISC) integrity. Nonetheless, as a perverse effect, maintenance of this program is likely to facilitate their neoplastic transformation and contribute to tumor initiation. We identified the quinolinate phosphoribosyltransferase enzyme (QPRT) as the main component of the ALEP-associated survival advantage. Here is mRNA expression data of second cohort of 50 sporadic primary colorectal carcinomas (CRC) resected from untreated patients used in conjunction with their QPRT values assessed by IHC. These 50 CRCs were scored for ALEP, Stem-like, Lgr5 and EphB2high signatures to test correlation with QPRT.

2021-05-06 | E-MTAB-4090 | 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