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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of breast cancer tumors of ductal and classical lobular types

ABSTRACT: Breast cancer tumors: of ductal (D) and classical lobular (L) type. Experiment "BC2_Jeffrey_minus_G50_1" was denoted as BC-D-002.

ORGANISM(S): Homo sapiens

SUBMITTER: Janos Demeter

PROVIDER: E-SMDB-3963 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Disease-specific genomic analysis: identifying the signature of pathologic biology.

Nicolau Monica M Tibshirani Robert R Børresen-Dale Anne-Lise AL Jeffrey Stefanie S SS

Bioinformatics (Oxford, England) 20070203 8

<h4>Motivation</h4>Genomic high-throughput technology generates massive data, providing opportunities to understand countless facets of the functioning genome. It also raises profound issues in identifying data relevant to the biology being studied.<h4>Results</h4>We introduce a method for the analysis of pathologic biology that unravels the disease characteristics of high dimensional data. The method, disease-specific genomic analysis (DSGA), is intended to precede standard techniques like clus ...[more]

PMID: 17277331

Similar Datasets

Transcription profiling of breast cancer tumors of ductal and lobular types

Project description:Breast cancer tumors of ductal (D) and lobular (L) type. Not all lobular tumors are "classical lobular" tumors. Experiment "BC2_Jeffrey_minus_G50_1" was denoted as BC-D-002.

2007-03-27 | E-SMDB-3962 | biostudies-arrayexpress

Transcription profiling of human lobular and ductal invasive carcinomas vs normal breast tissue from the same patient to identify gene expression profiles of ductal and lobular carcinomas in relation to normal ductal and lobular cells

Project description:The aim of our study was to identify gene expression profiles of ductal and lobular carcinomas in relation to normal ductal and lobular cells. We examined ten mastectomy specimens from postmenopausal breast cancer patients. Ductal and lobular tumor and normal cells were microdissected from cryosections. Fifty nanograms of total RNA were amplified and labeled by PCR and in vitro transcription. GCOS pairwise comparison algorithm and rank products have identified multiple genes that are differentially expressed in comparisons between ductal and lobular tumor and normal cell types. The results suggest that these genes are involved in epithelial-mesenchymal transition, TGFbeta and Wnt signaling. These changes are present in both tumor types but appear to be more prominent in lobular carcinomas. Ten surgical specimens obtained by mastectomy from postmenopausal patients with invasive ductal (IDC) and lobular breast (ILC) carcinomas were investigated. Of these, 5 were IDCs and 5 were ILCs. Tumor and normal tissues from the same mammary gland were identified by an experienced pathologist, snap-frozen in liquid nitrogen and stored at -80ÂºC for further analysis. Microdissection, RNA isolation, amplification, labeling and microarray analysis are described in sample definitions. Samples from particular cell types (normal ductal, normal lobular, tumor ductal, tumor lobular - 10, 10, 5, 5 samples, respectively) were considered as biological replicates and were compared in between.

2007-11-01 | E-GEOD-5764 | biostudies-arrayexpress

Analysis of microdissected invasive lobular and ductal breast carcinomas in relation to normal ductal and lobular cells

2007-03-16 | GSE5764 | GEO

Transcription profiling of breast cancer tumors of ductal and classical lobular types

Project description:Breast cancer tumors: of ductal (D) and classical lobular (L) type. Experiment "BC2_Jeffrey_minus_G50_1" was denoted as BC-D-002.

| S-ECPF-SMDB-3963 | biostudies-other

Characterisation of gene expression of cancer-associated and normal fibroblasts from lobular and ductal breast cancer patients

Project description:The purpose of this study was to characterise gene expression differences between cultured human cancer-associated fibroblasts and normal fibroblasts from lobular and ductal breast cancer patients.

2021-12-31 | GSE148156 | GEO

Transcription profiling of human invasive breast cancer carcinomas with different histological types and invasive lobular carcinoma

Project description:Gene expression array analysis on a series of ten different histological special types of invasive breast carcinomas (tubular, micropapillary, mucinous A, mucinous B, endocrine, apocrine, metaplastic, medullary, adenoid cystic, invasive ductal carcinoma with osteoclastic giant cells) and invasive lobular carcinoma.<br><br>Note: this experiment was reloaded into ArrayExpress in August 2010 to include mappings between raw and processed data files. It now includes additional dye-swap combined normalized data files.

2010-08-20 | E-NCMF-3 | biostudies-arrayexpress

Single cell transcriptomic heterogeneity in invasive ductal and lobular breast cancer cells

Project description:Single cell transcriptomic heterogeneity in invasive ductal and lobular breast cancer cells

| PRJNA603358 | ENA

Gene expression data from CD14++ CD16- classical monocytes from healthy volunteers and patients with pancreatic ductal adenocarcinoma

Project description:Transcriptomic profiling of peripheral immune cells can provide a wealth of information. Classical CD14++ CD16- monocytes were isolated from the peripheral blood of healthy volunteers and patients with pancreatic ductal adenocarcinoma and profiled for differential gene expression using Affymetrix human Genechips 2.1 U133. Differentially expressed genes were identified comparing gene expression profiles between healthy and PDAC.

2015-08-21 | E-GEOD-60601 | biostudies-arrayexpress

Gene expression data from CD14++ CD16- classical monocytes from healthy volunteers and patients with pancreatic ductal adenocarcinoma

2015-08-21 | GSE60601 | GEO

Single cell transcriptomic heterogeneity in invasive ductal and lobular breast cancer cells

Project description:Invasive lobular breast carcinoma (ILC), one of the major breast cancer histological subtypes, exhibits unique clinical and molecular features compared to the other well-studied ductal cancer subtype (IDC). The pathognomonic feature of ILC is loss of E-cadherin, mainly due to inactivating mutations within the CDH1 gene, but the extent of contribution of this genetic alteration to ILC-specific molecular characteristics remains largely understudied. To profile these features transcriptionally, we conducted single cell RNA sequencing on a panel of IDC and ILC cell lines, as well as an IDC cell line (T47D) with CRISPR-mediated knock out (KO) of CDH1. Inspection of intra-cell line heterogeneity illustrated genetically and transcriptionally distinct subpopulations in multiple cell lines and highlighted rare populations of cells with long latency and an apoptosis-related signature indicative of dormancy. Investigation of CDH1 KO-induced alterations showed transcriptomic membranous systems remodeling, elevated regulon activation resemblance of T47D CDH1 KO cells to ILCs, and suggests IRF1 as a major regulator of the pro-apoptotic and anti-proliferative feature of ILCs.

2020-11-05 | GSE144320 | GEO

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