Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Affymetrix - samples

ABSTRACT: Metabric breast cancer samples (Genotype raw data)

PROVIDER: EGAD00010000266 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Publications

Modelling the spatial heterogeneity and molecular correlates of lymphocytic infiltration in triple-negative breast cancer.

Yuan Yinyin Y

Journal of the Royal Society, Interface 20150201 103

Lymphocytic infiltration is associated with a favourable prognosis and predicts response to chemotherapy in many cancer types, including the aggressive triple-negative breast cancer (TNBC). However, it is not well understood owing to the high levels of spatial heterogeneity within tumours, which is difficult to analyse by traditional pathological assessment. This paper describes an unbiased methodology to statistically model the spatial distribution of lymphocytes among tumour cells based on aut ...[more]

PMID: 25505134

Similar Datasets

Illumina - samples

Project description:Metabric breast cancer samples (Expression raw data)

| EGAD00010000268 | EGA

RNA-seq data of canine mammary tumors and normal samples

Project description:Canine mammary gland tumors (CMTs) have been suggested as promising cancer models to human breast cancer due to their many biological and clinical similarities. Here, we collected 222 samples consist of 158 tumor samples and 64 matched normal samples of CMTs. Fresh tissue samples were transferred in to RNAlater, and refrigerated overnight at 4°C and then stored at -80°C. Total RNA was extracted from tissues using RNeasy mini kit. We aligned RNA-Seq raw data from 222 samples to canine reference genome CanFam3.1 using Tophat. We assembled transcript and calculated FPKM values using Cufflinks. All tumor samples were evaluated by histopathological characteristics including histopathological subtype, grade, and lymphatic invasion, and annotated with corresponding sequencing data. The histopathological classification and the histological grading system of CMTs were adopted from those of human breast cancer. In addition, immunohistochemical evaluation was performed in samples for estrogen receptor (ER) and human epidermal growth factor receptor 2 (HER2) status. DISCLAIMER: Using this dataset became freely available on Jul 22, 2019. On the other hand, we are now preparing a key paper about comparative analysis of canine and human breast cancer based on this dataset. If you plan to submit a similar paper using this dataset before the main paper is published, please feel free to contact the submitter (swkim@yuhs.ac) to coordinate submission.

2019-07-22 | GSE119810 | GEO

A pooled treatment-curated breast cancer gene-expression dataset

Project description:Pre-clinical studies reported the immunogenic or immunomodulatory effects of traditional cancer therapies. However, the publicly available well-curated and harmonized breast cancer datasets, such as TCGA, METABRIC, and MetaGxBreast, lack careful curation of treatment regimens. Hence, limited exploration of the impact of therapies on the prognostic/predictive value of breast cancer biomarkers. Herein, we describe a pooled and treatment-curated gene-expression dataset to investigate the impact of treatments on the prognostic/predictive value of biomarkers. We searched the gene expression omnibus database to identify potential human breast cancer gene-expression datasets with anthracycline/taxane treatment. Published datasets with the detailed treatment regimen, clinical endpoint, clinical-pathological, and gene-expression data were extracted and harmonized. The dataset described herein would help researchers explore the interaction between gene-expression biomarkers and immunogenic/immunomodulatory treatments in breast cancer.

2024-03-09 | GSE205568 | GEO

An assessment of prognostic immunity markers in breast cancer

Project description:We used Targeted RNA-seq to generate a gene expression data set of the 72-gene panel (TARGETSEQ) including 483 targeted RNA-seq data of 225 breast cancer FFPE samples from Shanghai and 258 breast cancer FFPE samples from UNC at Chapel Hill. The identified gene panel and risk evaluation model iRDM were developed in training data set AFFY1951 (p<0.0001, n=1951) and further validated in two other published gene expression datasets including Illumina beads array data METABRIC (p<0.0001, n=1997) and whole transcriptomic mRNA-seq data TCGA (p=0.00019, n=996) and in our own targeted RNA-seq data TARGETSEQ (p<0.0001, n=303) (of 483 RNA-seq samples, 303 with survival data). In conclusion, immunity gene expression were an important parameter for prognosis and therefore can be incorporated into current multi-gene assays to improve assessment of risk of distant metastasis in breast cancer.

2018-10-01 | GSE113863 | GEO

Mir-30e* is an independent subtype-specific prognostic marker in breast cancer

Project description:Both gene and miRNA expression patterns separately correlate with survival in breast cancer suggesting that the development of models using both miRNAs and gene markers might improve their prediction performance. In this study miRNAs significantly associated with development of distant metastasis were identified and further investigated and validated in the publicly available dataset from the METABRIC. A combined outcome prediction model using gene expression, miRNA expression and clinico-pathological features was implemented. Fresh-frozen primary tumors were obtained from 123 patients with operable breast cancer previously untreated, pathologically defined as axillary node-negative and undergoing radical or conservative surgery at the Istituto Nazionale Tumori of Milano (INTM) between1990 and 1998. Patients were selected in order to have a comparable pattern of classical risk factors (age, tumor size).

2015-07-31 | E-GEOD-59829 | biostudies-arrayexpress

Expression profiling of breast cancer samples from Institut Curie (Maire cohort) --Affy CDF

Project description:Transcriptome analysis of 130 breast cancer samples (41 TNBCÂ ; 30 Her2Â ; 30 Luminal B and 29 Luminal A), 11 normal breast tissue samples and 14 TNBC cell lines. This dataset contains 178 arrays. 153 arrays were used to analyze 130 unique breast cancer samples from as many patients and 23 technical duplicates. In addition 11 âNormalâ samples from healthy breast tissue obtained from mammoplasty are included, as well as a collection of 14 breast cancer cell lines. Data production involved different array batches and hybridation series which were accounted for in the pre-processing of the data.

2015-01-23 | E-GEOD-65194 | biostudies-arrayexpress

Images - samples

Project description:Metabric breast cancer samples (Images)

| EGAD00010000270 | EGA

Expression profiling of breast cancer samples from Institut Curie (Maire cohort) -- BrainArray CDF

Project description:Transcriptome analysis of 130 breast cancer samples (41 TNBCM-BM- ; 30 Her2M-BM- ; 30 Luminal B and 29 Luminal A), 11 normal breast tissue samples and 14 TNBC cell lines. This dataset contains 178 arrays. 153 arrays were used to analyze 130 unique breast cancer samples from as many patients and 23 technical duplicates. In addition 11 M-bM-^@M-^\NormalM-bM-^@M-^] samples from healthy breast tissue obtained from mammoplasty are included, as well as a collection of 14 breast cancer cell lines. Data production involved different array batches and hybridation series which were accounted for in the pre-processing of the data.

2015-01-23 | E-GEOD-65212 | biostudies-arrayexpress

Mir-30e* is an independent subtype-specific prognostic marker in breast cancer

2015-07-31 | GSE59829 | GEO

Expression profiling of invasive breast carcinoma samples from Institut Curie

Project description:Genomic hallmarks of homologous recombination deficiency in invasive breast carcinomas to appear in Internationa Journal of Cancer Transcriptome analysis of 243 (plus 12 duplicates) primary breast invasive carcinoma samples of various molecular subtypes. This dataset contains 255 arrays for 243 primary breast tumor samples obtained from 243 patient; 12 duplicated cases. Data production involved different array batches and hybridation series.

2015-06-19 | E-GEOD-69986 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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