Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression breast cancer

ABSTRACT: Gene expression profiles were generated from 176 primary breast cancer patients and 10 normal breast samples. This data is used to investigate the clinial relevance of genes of interest from in vitro studies, including FABP5 and DDX1.

ORGANISM(S): Homo sapiens

PROVIDER: GSE22820 | GEO | 2011/04/27

SECONDARY ACCESSION(S): PRJNA128101

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Gene expression breast cancer

Project description:Gene expression profiles were generated from 176 primary breast cancer patients and 12 normal breast samples. This data is used to investigate the clinical relevance of genes of interest from in vitro studies, including FABP5 and DDX1. This Series represents RNA isolated from 176 primary breast cancer patients and 10 normal breast samples. Gene expression is compared between various subgroups depending on their clinical parameters.

2011-04-27 | E-GEOD-22820 | biostudies-arrayexpress

Prediction of Breast Cancer Estrogen Receptor Status using Machine Learning

2013-01-01 | GSE29210 | GEO

Prediction of Breast Cancer Estrogen Receptor Status using Machine Learning

Project description:Gene expression profiles were generated from 199 primary breast cancer patients. Samples 1-176 were used in another study, GEO Series GSE22820, and form the training data set in this study. Sample numbers 200-222 form a validation set. This data is used to model a machine learning classifier for Estrogen Receptor Status. RNA was isolated from 199 primary breast cancer patients. A machine learning classifier was built to predict ER status using only three gene features.

2013-01-01 | E-GEOD-29210 | biostudies-arrayexpress

High-throughput sequencing analysis of mouse FABP5 KO BMDM cell transcriptomes with overexpression of FABP5 WT or FABP5 C127S after LPS treatment

Project description:Purpose: Mouse BMDM is the universal cell type of studying innate immunity. This study was designed to analyze LPS induced innate immune response and the gene expression in FABP5 KO BMDMs with overexpression of FABP5 WT or FABP5 C127S. Methods: FABP5 KO BMDMs were nucleofected with 5 μg pXJ40-3xFlag-FABP5 WT or C127S plasmid using the Amaxa Mouse Macrophage Nucleofector Kit (Lonza, VPA-1009) following the manufacturer’s instructions. Replace medium 6 hours post Nucleofection and add 500 ng/mL LPS to the fresh medium. 24 hours after treatment, harvest cells by using GenElute Single Cell RNA Purification Kit (Sigma, RNB300) and perform RNA-seq. Then mRNA profiles of these samples were generated by high-throughput sequencing analysis, using Illumina NovaSeq6000. And the differential mRNA profiles were analyzed. Results: mRNA profiles were analyzed, and differential expression profiles were compared. Conclusions: Our study demonstrated the transcriptional profiles of FABP5 KO BMDMs with overexpression of FABP5 WT or FABP5 C127S upon LPS treatment, with biologic replicates, generated by RNA-seq technology.

2021-11-01 | GSE182238 | GEO

Triple Negative Breast tumors: SPARC Positive Tumors vs SPARC Negative Tumors

Project description:The aim of this study was evaluate the transcriptome changes in the comparison between triple negative tumors with increased SPARC expression and triple negative tumors with decreased SPARC expression according to Nagai et al., 2011 (Breast Cancer Res Treat (2011) 126:1–14) The results generated could be of particular interest to better define the prognostic impact of SPARC expression in triple negative breast tumors

2018-07-01 | GSE98931 | GEO

Characterization and clinical evaluation of CD10+ stroma cells in the breast cancer microenvironment

Project description:Purpose: There is growing evidence that interaction between stromal and tumor cells is pivotal in breast cancer progression and response to therapy. Since the pioneer work of Allinen et al. suggested that during breast cancer progression striking changes occur in CD10+ stromal cells, we aimed to better characterize this cell population and its clinical relevance. Results: This 12-gene CD10+ stroma signature includes among others genes involved in matrix remodeling (MMP11, MMP13, COL10A1) and genes related to osteoblast differentiation (periostin). The co-culture experiments demonstrated all three CD10+ cell types contribute to the CD10+ stroma signature. Of interest, this signature demonstrated an important role in differentiating in situ from invasive breast cancer, in prognosis of the HER2+ subpopulation of breast cancer only, and potentially in non-response to chemotherapy for those patients. Conclusions: Our results highlight the importance of CD10+ cells in breast cancer prognosis and efficacy of chemotherapy, particularly within the HER2+ breast cancer disease.

2012-03-15 | GSE27120 | GEO

Deconvolution of breast tumors for optimal chemotherapy selection

Project description:Extensive work in pre-clinical models has shown that microenvironmental cells influence many aspects of cancer cell behavior including metastatic potential and their sensitivity to therapeutics. In the human setting, this behavior is mainly correlated with the presence of immune cells, whilst the relevance of other cell types have been largely ignored. Here, in addition to T cells, B cells, macrophages and mast cells, we identified the relevance of non-immune cell types for breast cancer survival and therapy benefit, including fibroblast, myoepithelial cells, muscle cells, endothelial cells, and 7 distinct epithelial cell types. Using single-cell sequencing data, we generated reference profiles for all these cell types. We used these reference profiles in deconvolution algorithms to optimally detangle the cellular composition of over 3500 primary breast tumors of patients that were enrolled in the SCAN-B and MATADOR clinical trials, and for which bulk mRNA sequencing data was available. This large data set enables us to identify and subsequently validate the cellular composition of microenvironments that distinguish differential survival and treatment benefit for different treatment regiments in primary breast cancer patients.

2021-12-10 | GSE168410 | GEO

Clinical Relevance of estrogen reactivity in the breast cancer microenvironment

Project description:Clinical Relevance of estrogen reactivity in the breast cancer microenvironment

| PRJNA818635 | ENA

DDX1 regulates alternative splicing and insulin secretion in pancreatic β cells

Project description:DEAD-box helicase 1 (DDX1) is a multifunction protein involved in diverse cellular processes including transcription, viral replication, mRNA/miRNA processing, and tRNA splicing. Here, we report a novel function of DDX1 in mRNA alternative splicing in pancreatic β cells. By performing integrated data analysis of high-throughput RNA sequencing (RNA-Seq), and cross-linking and immunoprecipitation coupled with deep sequencing (CLIP-Seq), we identify hundreds of alternative splicing genes that are targeted by DDX1. These DDX1-targeted alternative splicing genes are mainly associated with calcium ion binding, high voltage-gated calcium channel, and transmembrane transporter. Functionally, silencing DDX1 impairs calcium influx and insulin secretion in the pancreatic β cells. These results reveal an important role for DDX1 in the regulation of gene alternative splicing and insulin secretion in pancreatic β cells.

2018-05-02 | GSE113893 | GEO

TUMOUR KINOME RE-WIRING GOVERNS RESISTANCE TO PALBOCICLIB IN OESTROGEN RECEPTOR POSITIVE BREAST CANCERS, HIGHLIGHTING NEW THERAPEUTIC MODALITIES

Project description:Estrogen receptor positive (ER+) breast cancers are the most common type of breast cancer. Despite the great efficacy of endocrine therapies, resistance remains a problem. Therefore, there is an immediate need for new, effective therapies in ER+ BC. In this study, we have explored the role of a potent CDK4/6 inhibitor called palbociclib. In order to identify differential phosphoproteomic events that underpin the mode of action and recurrence for this treatment, we generated a panel of palbociclib-sensitive and resistant cell lines and did quantitative, shotgun phosphoproteomics using titanium IMAC. Palbociclib sensitive cell lines (wt-MCF7 or MCF7-LTED) were cultured in phenol red-free RPMI supplemented with 10% FBS and 1nM estradiol or 10% dextran-coated charcoal (DCC) respectively. Thereafter, palbociclib resistant cell lines were generated using 1μΜ palbociclib concentration. Samples were harvested at baseline and at the point of resistance.

2020-04-29 | PXD005514 | Pride

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