Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

11 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Human breast cancer cell line temporal response to Hepatocyte growth factor / scatter factor (HGF/SF)

ABSTRACT: To study the gene expression kinetics following activation of Met, one normal human breast epithelium and six human breast cancer cell lines with variable Met expression and activity, were treated with HGF/SF for 0, 10, 30min and 24 hours and subjected to cDNA array analysis

ORGANISM(S): Homo Sapiens

SUBMITTER: Gideon Stein

PROVIDER: E-MTAB-762 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Met kinetic signature derived from the response to HGF/SF in a cellular model predicts breast cancer patient survival.

Stein Gideon Y GY Yosef Nir N Reichman Hadar H Horev Judith J Laser-Azogui Adi A Berens Angelique A Resau James J Ruppin Eytan E Sharan Roded R Tsarfaty Ilan I

PloS one 20120925 9

To determine the signaling pathways leading from Met activation to metastasis and poor prognosis, we measured the kinetic gene alterations in breast cancer cell lines in response to HGF/SF. Using a network inference tool we analyzed the putative protein-protein interaction pathways leading from Met to these genes and studied their specificity to Met and prognostic potential. We identified a Met kinetic signature consisting of 131 genes. The signature correlates with Met activation and with respo ...[more]

PMID: 23049908

Similar Datasets

Mimp/Mtch2-GFP overexpression in transgenic mice kidney

Project description:Metabolic dysfunctions, such as fatty liver, obesity and insulin resistance, are among the most common contemporary diseases worldwide. Mimp/Mtch2 is a mitochondrial carrier protein homologue that leads to mitochondrial depolarization, localizes to the mitochondria and induces accumulation of fat vesicles. Transgenic mice overexpressing Mimp/Mtch2 develop fatty livers and kidneys and exhibit high blood glucose levels. The mechanism of lipid accumulation in the kidney has not been fully determined. In this study we performed a differential gene expression profile of fatty compared to non-fatty kidneys of Mimp/Mtch2-GFP transgenic mice, fed on high fat diet. RNA samples for microarray gene expression profiling were obtained from four Mimp/Mtch2-GFP mice, two samples of low fat kidneys and two of fatty kidneys.

2016-06-15 | E-MTAB-1752 | biostudies-arrayexpress

Clinical and prognostic relevance of squalene epoxidase in breast cancer

Project description:All cell lines were purchased from ATCC (LGC Standards S.r.l., Milan, Italy), except T-47D and MDA-MB-468 that were obtained from the National Cancer Institute Developmental Therapeutics Program (Frederick, MD). Six untreated breast cancer cell lines grown according to the growth protocol reported below

2015-07-28 | E-GEOD-71395 | biostudies-arrayexpress

Integrated mutation, copy number and expression profiling in resectable non-small cell lung cancer

Project description:Study aims: to identify critical genes involved in non-small cell lung cancer (NSCLC) pathogenesis that may lead to a more complete understanding of this disease and identify novel molecular targets for use in the development of more effective therapies. Methods: Both transcriptional and genomic profiling were performed on 69 resected NSCLC specimens and results correlated with mutational analyses and clinical data to identify genetic alterations associated with groups of interest. Results: Combined analyses identified specific patterns of genetic alteration associated with adenocarcinoma vs. squamous differentiation; KRAS mutation; TP53 mutation, metastatic potential and disease recurrence and survival. Amplification of 3q was associated with mutations in TP53 in adenocarcinoma. A prognostic signature for disease recurrence, reflecting KRAS pathway activation, was validated in an independent test set. Conclusions: These results may provide the first steps in identifying new predictive biomarkers and targets for novel therapies, thus improving outcomes for patients with this deadly disease. Transcriptional profiling of 82 samples of NSCLC using Peter MacCallum in-house 10,500 element cDNA microarray. RNA from 11 pooled cell lines used as reference for each sample. Replicate of 6 samples included.

2010-11-27 | E-GEOD-25326 | biostudies-arrayexpress

Transcription profiling of in vivo range finding studies in the rat with selected individual food additives

Project description:FSAT01021/OBJ01/28D: TITLE: Development of methods for the assessment of the health effects from mixtures of food additives. SAP/S3 project code: 010.45073 TNO Voeding-TNO BIBRA project for UK Food Standard Agency Objective No. 01: In vivo range finding studies in the rat with selected individual food additives. Rat study using 4 compounds, oral administration in diet (concentration given in ppm), for 28 days: Butylated hydroxytoluene (BHT): 254 ppm; 762 ppm; 1523 ppm; 3046 ppm; 10154 ppm Curcumin (CC): 254 ppm; 762 ppm; 2031 ppm; 4062 ppm; 10154 ppm Propyl Gallate (PG): 203 ppm; 508 ppm; 1523 ppm; 3046 ppm; 6092 ppm Thiabendazole (TB): 102 ppm; 254 ppm; 762 ppm; 2031 ppm; 5077 ppm Within Objective No. 01: clinical chemistry, pathology, drug metabolizing enzymes are assessed as well. Within Objective No. 01: A smaller study in which rats were exposed for 3 days to two doses of BHT, CC, PG, TB was performed as well. Depending on the outcome of arrays performed within FSAT01021/OBJ01/28D, transcriptomics will be performed on these samples: the Experiment name then will be FSAT01021/OBJ01/3D for details: Rob Stierum , AVTO, Monday December 17th 2001

2008-06-09 | E-MEXP-116 | biostudies-arrayexpress

Inhibition of Met results in concomitant inhibition of Akt and STAT3 signaling pathways, while abrogation of negative feedback permits Erk reactivation

Project description:Amplification and activation of the Met receptor tyrosine kinase occurs up to 23% of gastric cancers, suggesting that Met is a therapeutic target in these cancers. However, the steady-state signaling events that occur during chronic Met activation, and mechanisms for resistance to Met small-molecule inhibitors, are poorly understood. Here we show that multiple gastric cancer cell lines harboring MET amplifications are dependent on Met signaling for proliferation and anchorage-independent growth. In these cells, short-term inhibition of Met leads to coordinated changes in gene expression; these include a rapid loss in expression of immediate-early genes, followed by decreased expression of genes involved in cell cycle and proliferation. Activation of Ras-Erk, PI3K-Akt and STAT3 pathways is attenuated by acute Met inhibition. STAT3 inhibition alone, but not individual inhibition of Mek or Akt, is sufficient to abrogate Met-dependent growth of these cells. However, following chronic Met inhibition, reactivation of Mek-dependent Erk phosphorylation occurs even in the presence of Met inhibitor corresponding with a downregulation of Erk negative regulators DUSP4/6. This provides a mechanism for the emergence of drug resistance. Our findings provide insights into innate resistance to a small-molecule Met inhibitor and highlight rational combination therapies that could be evaluated in clinical trials. Time series experiment, four cell lines, 2 treatments

2014-05-19 | E-GEOD-54532 | biostudies-arrayexpress

Mosaic Amplification of Multiple Receptor Tyrosine Kinase Genes in Glioblastoma

Project description:Here we present a novel example of genetic heterogeneity in human malignant brain tumors, in which multiple closely-related driver genes are amplified and activated simultaneously in adjacent intermingled cells. We have observed up to 3 different receptor tyrosine kinases (EGFR, MET, PDGFRA) amplified in single tumors in different cells in a mutually exclusive fashion. However, these subpopulations cannot be always observed with a genome wide studies such as aCGH. Here we include aCGH on three such mosaic cases. Analyses were performed on 350 archival specimens of glioblastoma, WHO Grade IV, seen at the Department of Pathology, Massachusetts General Hospital from 2009 to 2011. CGH on three such mosaic cases.

2012-01-01 | E-GEOD-33483 | biostudies-arrayexpress

Changes in gene expression during epithelial-mesenchymal transition in a breast cancer primary culture

Project description:Epithelial-Mesenchymal Transition (EMT) is an important process during normal development, but also co-opted by various cancer cells to enable them to invade and form metastases at distant sites. In this study, we examinated changes in gene expression during EMT in breast cancer using primary culture named BCpc. Changes in gene expression in primary cells from breast tumour specimen (named BCpc) were analyzed as two-color hybridizations using Agilent Technologies whole human genome 4x44K microarrays

2014-06-02 | E-GEOD-53175 | biostudies-arrayexpress

Gene expression profiling of IOERT exposed MCF10A breast epithelial cells

Project description:Intraoperative Electron Radiation Therapy (IOERT) is a therapeutic technique that delivers a single high dose of ionizing radiation (IR) directly to the tumor bed during cancer surgery. The main goal of IOERT is to counteract tumor growth by acting on residual cancer cells in the site at high risk for recurrence as well as to preserve healthy surrounding tissue from the side effects of radiation therapy. The high IR dose used during IOERT treatment induces a strong stress response resulting in the activation of pro- and anti-proliferative cell signaling pathways in both tumor and normal cells. The radiobiology of healthy tissue response to IR is a topic of interest which may contribute to avoid the impairment of normal tissue/organ function and to decrease the risks of secondary cancers. In this study, we examined changes in gene expression in MCF10A breast epithelial cell line exposed to 9Gy and 23Gy high single dose of IR delivered by IOERT. Changes in gene expression in MCF10A breast epithelial cell line exposed to 9Gy and 23Gy high single dose of IR (named MCF10A_9Gy and MCF10A_23Gy respectively), were analyzed as two-color hybridizations using Agilent Technologies whole human genome 4x44K microarrays

2015-07-06 | E-GEOD-65954 | biostudies-arrayexpress

Gene expression response to high radiation treatment in MCF7 breast cancer cell line

Project description:Intraoperative radiotherapy (IOERT) is a high radiation therapeutic technique which administers a single high dose of ionizing radiation (IR) immediately after surgical tumor removal in order to destroy the residual cancer cells in the site at high risk for recurrence. IR is able to regulate several genes and factors involved in cell-cycle progression, survival and/or cell death, DNA repair and inflammation modulating an intracellular response radiation dependent producing an imbalance in cell fate decision. In this study, we examined changes in gene expression in MCF7 breast cancer cell line exposed to 9Gy and 23Gy high single dose of IR delivered by IOERT. Changes in gene expression in MCF7 breast cancer cell line exposed to 9Gy and 23Gy high single dose of IR (named MCF7_9Gy and MCF7_23Gy respectively), were analyzed as two-color hybridizations using Agilent Technologies whole human genome 4x44K microarrays

2015-06-11 | E-GEOD-63667 | biostudies-arrayexpress

Copy number variation analysis of 16HBE14o- and T84 cell lines

Project description:The aim of the project was to detect genomic regions that were normal, duplicated or deleted in these cell lines for transcription factors NFKBp50, NFkBp65, HIF1a and FAS gene which we studied. It is not clear the effects of copy number variations on allele specific assembly or disruption of master regulator transcription factors. Thus, the CNV analysis verified that 16HBE cell line, though transformed with defective simian virus, had normal copy number variations thus was a suitable source for nuclear extract to study the afore mentioned TFs. T84 showed duplications and large genomic deletions for TFs: NFkBp50 and p65. 16HBE and T84 are both epithelial cell lines type from human. 16HBE is derived from bronchial epithelium, while the T84 is derived from the colon carcinoma.

2016-09-22 | E-MTAB-4194 | 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