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Series GSE16070 Query DataSets for GSE16070
Status Public on Sep 08, 2009
Title Networking of differentially expressed genes in human MCF7 breast cancer cells resistant to methotrexate
Organism Homo sapiens
Experiment type Expression profiling by array
Summary A summary of the work associated to these microarrays is the following:

The need for an integrated view of all data obtained from high-throughput technologies gave rise to network analyses. These are especially useful to rationalize phenomena in terms of how external perturbations propagate through the expression of genes. To address this issue in the case of drug resistance, we constructed Biological Association Networks of genes differentially expressed in cell lines resistant to methotrexate (MTX). Seven cell lines representative of different types of cancer including colon cancer (HT29 and Caco2), breast cancer (MCF7 and MDA-MB-468), pancreatic cancer (MIA PaCa-2), erythroblastic leukemia (K562) and osteosarcoma (Saos-2), were used. The differential expression pattern between sensitive and MTX-resistant cells was determined by microarrays covering the whole human genome and analyzed with the GeneSpring GX software package, v.7.3.1. Genes deregulated in common in the two colon cancer cell lines studied, were subject of Biological Association Networks construction. Dikkopf homolog-1 (DKK1) was a clear node of this network, and functional validations of this target using a siRNA showed a chemosensitization toward MTX. Members of the UDP-glucuronosyltransferase 1A (UGT1A) family formed a network of differentially expressed genes in the two breast cancer cell lines studied. siRNA treatment against UGT1A showed also an increase in MTX sensitivity. Eukaryotic translation elongation factor 1 alpha 1 (EEF1A1) was a gene overexpressed in common among the pancreatic cancer, leukemia and osteosarcoma cell lines, and siRNA treatment against EEF1A1 produced a chemosensitization toward MTX. Biological Association Networks identified DKK1, UGT1As and EEF1A1 as important gene nodes in MTX-resistance. Treatments using iRNA technology against these three genes show chemosensitization toward MTX.
 
Overall design Two cell lines are compared, which are MCF7 breast cancer cells sensitive to methotrexate and MCF7 cells resistant to 10e-6M methotrexate. Six samples are provided which correspond to tripicates of each cell line. The samples provided were analyzed using the specific software GeneSpring GX.
 
Contributor(s) Selga E, Oleaga C, de Almagro M, Noé V, Ciudad CJ
Citation(s) 19732436
Submission date May 12, 2009
Last update date Mar 25, 2019
Contact name Carlos J Ciudad
E-mail(s) cciudad@ub.edu
Phone +34-93-403-4455
Organization name University of Barcelona
Department Biochemistry and Molecular Biology
Lab School of Pharmacy
Street address Av. Juan XXIII-27
City Barcelona
State/province Barcelona
ZIP/Postal code 08028
Country Spain
 
Platforms (1)
GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
Samples (6)
GSM402417 MCF7 parental cells replicate 1
GSM402418 MCF7 parental cells replicate 2
GSM402419 MCF7 parental cells replicate 3
This SubSeries is part of SuperSeries:
GSE16648 Networking of differentially expressed genes in human cancer cell lines resistant to methotrexate
Relations
BioProject PRJNA123095

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE16070_RAW.tar 46.9 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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