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Series GSE23884 Query DataSets for GSE23884
Status Public on Dec 01, 2010
Title An Integrated Approach to Uncover Drivers of Cancer
Organism Homo sapiens
Experiment type Expression profiling by array
Summary We developed a computational framework that integrates chromosomal copy number and gene expression data for detecting aberrations that promote cancer progression. We demonstrate the utility of this framework using a melanoma dataset. Our analysis correctly identified known drivers of melanoma and predicted multiple novel tumor dependencies. Two dependencies, TBC1D16 and RAB27A, confirmed empirically, suggest that abnormal regulation of protein trafficking contributes to proliferation in melanoma. Together, these results demonstrate the ability of integrative Bayesian approaches to identify novel candidate drivers with biological, and possibly therapeutic, importance in cancer.
 
Overall design Effects of knockdown of two genes -TBC1D16 and RAB27A - were tested on four cell lines each, each of them with two different hairpins. As a control, we used a hairping targeting GFP. shGFP experiments were done in biological duplicates or more. The second WM1976-shGFP sample was identified as an outlier by a PCA analysis and was excluded from our analysis.
 
Contributor(s) Akavia U, Litvin O, Kim J, Sanchez-Garcia F, Kotliar D, Causton HC, Pochanard P, Mozes E, Garraway LA, Pe'er D
Citation(s) 21129771
Submission date Aug 31, 2010
Last update date Jul 26, 2018
Contact name Dana Pe'er
Organization name Columbia University
Department Biological Sciences
Lab Dana Pe'er
Street address 1212 Amsterdam Ave.
City New York
State/province NY
ZIP/Postal code 10027
Country USA
 
Platforms (1)
GPL6244 [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version]
Samples (31)
GSM589042 A375-sh477
GSM589043 A375-sh865
GSM589044 A375-shGFP1
Relations
BioProject PRJNA130499

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
GSE23884_FoldChange.txt.gz 810.1 Kb (ftp)(http) TXT
GSE23884_RAW.tar 147.8 Mb (http)(custom) TAR (of CEL)
GSE23884_probeset2gene.txt.gz 123.7 Kb (ftp)(http) TXT
Processed data included within Sample table

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