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Series GSE50564

Query DataSets for GSE50564

Status

Public on Sep 07, 2013

Title

IMPACT: Unraveling intracellular signal transduction and pathway crosstalk by exploring pathway landscape

Organism

Homo sapiens

Experiment type

Expression profiling by array
Third-party reanalysis

Summary

Understanding complicated modularization and crosstalk of intracellular signal transduction pathways holds the key to battle against drug resistance in human cancer research. We propose an integrative approach, namely Inferring Modularization of PAthway CrossTalk (IMPACT), to identify aberrant pathway modules and their between-module crosstalk by exploring pathway landscape that is reconstructed from a sampling strategy. The pathway identification method (i.e., IMPACT) was applied to breast cancer data to uncover aberrant pathway modules, which were further investigated with cell line studies to understand drug resistance in breast cancer.

The patient datasets we mentioned are published and are available in the GEO database as GSE6532 and GSE17705.

The re-processed GSE6532 and GSE17705 patient datasets are linked below as supplementary files. The GSE6532_matrix.txt and GSE17705_matrix.txt are processed by Affy Gene console with plier as normailization. But importantly, we also used 'Combat' method (http://www.bu.edu/jlab/wp-assets/ComBat/Abstract.html) to remove potential institutional batch effect.

Overall design

Four MCF7 derived cell models were included in the study: MCF7-STR, MCF7RR-STR, LCC1 and LCC2 cell lines. MCF7-STR and MCF7RR-STR were grown in phenol red-free IMEM supplemented with 5% charcoal-stripped calf serum and 1nM estradiol for 72 h prior to RNA extraction. LCC1 and LCC2 cells were grown in phenol red-free IMEM supplemented with 5% charcoal-stripped calf serum. The cell line data were used to validate computational results derived from patient datasets.

Contributor(s)

Gu J, Xuan J, Shajahan-Haq AN, Demas DM, Wang Y, Clarke R

Citation missing

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Submission date

Sep 04, 2013

Last update date

Mar 25, 2019

Contact name

Jinghua Gu

E-mail(s)

[email protected]

Organization name

Virginia Tech

Street address

900 N.Glebe Rd

City

Arlington

ZIP/Postal code

22203

Country

USA

Platforms (1)

GPL570

[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array

Samples (12)

More...

GSM1223623	MCF7-2-STR-P58
GSM1223624	MCF7-2-STR-P59
GSM1223625	MCF7-2-STR-P60

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BioProject

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary file	Size	Download	File type/resource
GSE50564_GSE17705_matrix.txt.gz	10.4 Mb	(ftp)(http)	TXT
GSE50564_GSE6532_matrix.txt.gz	21.7 Mb	(ftp)(http)	TXT
GSE50564_RAW.tar	56.2 Mb	(http)(custom)	TAR (of CEL)
Processed data included within Sample table
Processed data are available on Series record