Transcriptomics

Dataset Information

7

CytoScanHD array Data for Colerectal Tumor and Normal Samples


ABSTRACT: 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. 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.

ORGANISM(S): Homo sapiens  

SUBMITTER: Ebtehal Al Sheikh   Mishal Johani  Maha Al Rodayyan  Sabeena Mustafa  Hisham Eldai  Zeyad Yousef  Mohammed A Khan  Sathish Periyasamy  Saeed Al Qarni  Mohammad A Aziz 

PROVIDER: E-GEOD-47204 | ArrayExpress | 2013-09-01

SECONDARY ACCESSION(S): GSE47204PRJNA205093

REPOSITORIES: GEO, ArrayExpress

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