Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression profile of breast cancer cells.

ABSTRACT: We compared the gene expression profile of 26 breast cancer cell lines to identify variations associated with different phenotypes and molecular subtype. The panel includes 13 estrogen receptor negative (ER-) and 13 ER+ cell lines. Four of the ER- cell lines and 5 of the ER+ cell lines are HER2 positive. We have used 2-color gene expression arrays for two separate studies. The one described here compares the intensities of one color channel across 26 cell lines, as normalized signal intensities. The second color channel is not analyzed here and will be used in a separate study.

ORGANISM(S): Homo sapiens

SUBMITTER: Francescopaolo Di Cello

PROVIDER: E-GEOD-44836 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Methylation of the claudin 1 promoter is associated with loss of expression in estrogen receptor positive breast cancer.

Di Cello Francescopaolo F Cope Leslie L Li Huili H Jeschke Jana J Wang Wei W Baylin Stephen B SB Zahnow Cynthia A CA

PloS one 20130703 7

Downregulation of the tight junction protein claudin 1 is a frequent event in breast cancer and is associated with recurrence, metastasis, and reduced survival, suggesting a tumor suppressor role for this protein. Tumor suppressor genes are often epigenetically silenced in cancer. Downregulation of claudin 1 via DNA promoter methylation may thus be an important determinant in breast cancer development and progression. To investigate if silencing of claudin 1 has an epigenetic etiology in breast ...[more]

PMID: 23844228

Similar Datasets

Gene methylation profile of breast cancer cells.

Project description:We compared the gene methylation profile of 26 breast cancer cell lines to identify variations associated with different phenotypes and molecular subtype. The panel includes 13 estrogen receptor negative (ER-) and 13 ER+ cell lines. Four of the ER- cell lines and 5 of the ER+ cell lines are HER2 positive. Bisulphite converted DNA from the 26 samples was hybridised to the Illumina Infinium Human Methylation450 Beadchip.

2013-07-12 | E-GEOD-44837 | biostudies-arrayexpress

Gene methylation profile of breast cancer cells.

2013-07-12 | GSE44837 | GEO

Gene expression profile of breast cancer cells.

Project description:We compared the gene expression profile of 26 breast cancer cell lines to identify variations associated with different phenotypes and molecular subtype. The panel includes 13 estrogen receptor negative (ER-) and 13 ER+ cell lines. Four of the ER- cell lines and 5 of the ER+ cell lines are HER2 positive.

2013-07-12 | GSE44836 | GEO

Comparision of gene expression in miR-17-92 cluster overexpression stable CCLP-1 cells with scrambled control CCLP-1 cells

Project description:To further development of our gene expression approach, we have employed whole genome microarray expression profiling as a discovery platform to identify genes which may be regulated by miR-17-92 cluster. Two stable cell lines were used, one is scrambled control and another is miR-17-92 cluster overexpresion cell lines. The differential gene expression was identified. Total RNA were extracted from two samples from the cell lines.

2014-05-31 | E-GEOD-58060 | biostudies-arrayexpress

In vitro pigmentation of human iPSC-derived retinal pigment epithelium cells is not indicative of their quality for cell transplantation

Project description:Retinal pigment epithelium (RPE) cells show heterogeneous level of pigmentation when cultured in vitro. We used Automated Live imaging and cell Picking System (ALPS) with single cell RNA sequencing (scRNA-seq) to analyze the correlation between color intensities and gene expression profiles of human-induced pluripotent stem (iPS) cell-derived RPE cells.

2024-05-04 | GSE242184 | GEO

Mitotic chromatin proteomics - Proteomics analysis with a nano Random Forest approach reveals novel functional interactions regulated by SMC complexes on mitotic chromosomes

Project description:we used stable isotope labeling with amino acids in cell culture (SILAC) to compare the proteomes of mitotic chromosomes isolated from cell lines harboring conditional knockouts of members of the condensin (SMC2, CAP-H, CAP-D3), cohesin (Scc1/Rad21), and SMC5/6 (SMC5) complexes.

2016-05-31 | PXD003427 | Pride

MicroRNA and mRNA expression profiles of hepatobiliary tumor patients' tissue together with those of non-tumor part tissues and serum exosomes. (mRNA)

Project description:10 cholangiocarcinoma (including 4 younger cases) and 14 control (10 hepatocellular carcinomas and 4 benigns) patients' tumor and non-tumor parts were obtained and then devided into 8 groups. Total RNA were extracted and purified from tissues and microRNA signal intensities are measured using Toray 3D gene microarrays designed for expression profiles. mRNA signal intensities were measured using agilent one color microarrays designed for expression profiles.

2022-09-16 | GSE209874 | GEO

MicroRNA and mRNA expression profiles of hepatobiliary tumor patients' tissue together with those of non-tumor part tissues and serum exosomes. (miRNA)

2022-09-16 | GSE209611 | GEO

Gene expression in mouse retinas with cone cyclic nucleotide gated channel deficiencies

Project description:The cone photoreceptor cyclic nucleotide-gated (CNG) channel is essential for central and color vision and visual acuity. Mutations in the channel subunits CNGA3 and CNGB3 are associated with achromatopsia and cone dystrophy. We investigated the gene expression profiles in mouse retina with CNG channel deficiency on a cone-dominant background, i.e., CNGA3-/-/Nrl-/- and CNGB3-/-/Nrl-/- mice, relative to Nrl-/- mice.

2013-07-03 | GSE40982 | GEO

The ets transcription factor ELF5 suppresses the estrogen sensitive phenotype and contributes to antiestrogen resistance in luminal breast cancer. [mouse]

Project description:The ets transcription factor ELF5 specifies the differentiation of mammary progenitor cells to establish the milk-secreting lineage. ER- and poor prognosis basal breast cancers arise from this progenitor cell and these cancers express high levels of Elf5. Knockdown of ELF5 expression in basal breast cancer cell lines, or forced expression in luminal breast cancer cell lines, resulted in reduced cell proliferation. Transcript profiling and chromatin immunoprecipitation revealed that the transcriptional activity of ELF5 specified the gene expression patterns that distinguish basal from luminal breast cancer, including suppression of FOXA1, GATA3 and ER, key estrogen-action genes. Tamoxifen treatment of luminal MCF7 cells upregulated Elf5 expression and cells that acquired resistance to Tamoxifen became dependent on ELF5 for proliferation. ELF5 is a regulator of breast cancer cell proliferation, transcriptionally specifies the basal molecular subtype and is utilised by ER+ breast cancer cells to escape proliferative arrest caused by Tamoxifen. Elf5 was induced via doxycycline treated PyMT mouse tumours, in triplicate

2014-01-13 | E-GEOD-30406 | 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