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Series GSE47204 Query DataSets for GSE47204
Status Public on Sep 01, 2013
Title CytoScanHD array Data for Colerectal Tumor and Normal Samples
Organism Homo sapiens
Experiment type Genome variation profiling by genome tiling array
Genome variation profiling by SNP array
Summary Genomic abnormalities leading to colorectal cancer (CRC) include somatic events causing copy number aberrations (CNAs) as well as copy neutral manifestations such as loss of heterozygosity (LOH) and uniparental disomy (UPD). We studied the causal effect of these events by analyzing high resolution cytogenetic microarray data of 15 tumor-normal paired samples. We detected 144 genes affected by CNAs. A subset of 91 genes are known to be CRC related yet high GISTIC scores indicate 24 genes on chromosomes 7, 8, 18 and 20 to be strongly relevant. Combining GISTIC ranking with functional analyses and degree of loss/gain we identify three genes in regions of significant loss (ATP8B1, NARS, and ATP5A1) and eight in regions of gain (CTCFL, SPO11, ZNF217, PLEKHA8, HOXA3, GPNMB, IGF2BP3 and PCAT1) as novel in their association with CRC. Pathway analysis indicates TGF-β signaling pathway to be affected by the cytogenetic events causing CRC as evidenced by the action of genes impacted by CNAs on SMAD family of proteins. Finally, LOH and UPD collectively affected nine cancer related genes. Transcription factor binding sites on regions of >35% copy number loss/gain influenced 16 CRC genes. Our analysis shows patient specific CRC manifestations at the genomic level and that these different events affect individual CRC patients differently.
 
Overall design Copy number analysis of Affymetrix CytoScanHD arrays was performed for 15 Tumors and 15 Adjacent Normals from Colorectal Tissue was used as reference for the study.
 
Contributor(s) Eldai H, Periyasamy S, Aziz MA, Al Qarni S, Al Rodayyan M, Mustafa S, Al Sheikh E, Khan MA, Johani M, Yousef Z
Citation(s) 24204606
Submission date May 22, 2013
Last update date Jul 13, 2018
Contact name Sathish Periyasamy
E-mail(s) sathish.periyasamy@gmail.com
Phone 0966503921073
Organization name NGHA
Department Bioinformatics
Street address P.O. Box 22490
City Riyadh
State/province Select a State or Province
ZIP/Postal code 11426
Country Saudi Arabia
 
Platforms (1)
GPL16131 [CytoScanHD_Array] Affymetrix CytoScan HD Array
Samples (30)
GSM1146803 Colorectal Normal Tissue-011112-01NB-CytoScanHD
GSM1146804 Colorectal Normal Tissue-031912-01NB-CytoScanHD
GSM1146805 Colorectal Normal Tissue-033112-01NB-CytoScanHD
Relations
BioProject PRJNA205093

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
GSE47204_Matrix_Processed_data.txt.gz 32.2 Kb (ftp)(http) TXT
GSE47204_RAW.tar 922.2 Mb (http)(custom) TAR (of CEL)
Processed data are available on Series record
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