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Identification of genes with correlated patterns of variations in DNA copy number and gene expression level in gastric cancer

 Sanghwa Yang  ;  Hei-Cheul Jeung  ;  Hyun Cheol Chung  ;  Woo Ick Yang  ;  Sun Young Rha  ;  Jae-Joon Jung  ;  Ji Eun Kim  ;  Yeon Ho Choi  ;  Ha Jin Jeong 
 GENOMICS, Vol.89(4) : 451-459, 2007 
Journal Title
Issue Date
Cluster Analysis ; Gene Dosage* ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic* ; Genes, Tumor Suppressor ; Genomics ; Humans ; Nucleic Acid Hybridization ; Oligonucleotide Array Sequence Analysis ; Oncogenes ; Stomach Neoplasms/genetics*
To identify DNA copy number changes that had a direct influence on mRNA expression in gastric cancer, cDNA microarray-based comparative genomic hybridization (aCGH) and gene expression profiling were performed using 17 K cDNA microarrays. A set of 158 genes showing Pearson correlation coefficients over 0.6 between DNA copy number changes and mRNA expression level variations was selected. In an independent gene expression profiling of 60 tissue samples, the 158 genes were able to distinguish most of the normal and tumor tissues in an unsupervised hierarchical clustering, suggesting that the differential expression patterns displayed by this specific group of genes are most likely based on the gene copy number changes. Furthermore, 43 statistically significant (P < 0.01) genes were selected that correctly distinguished all of the tissue samples. The copy number changes detected by aCGH can be verified by fluorescence in situ hybridization and real-time polymerase chain reaction. The selected genes include those that were previously identified as being tumor suppressors or deleted in various tumors, including GATA binding protein 4 (GATA4), monoamine oxidase A (MAOA), cyclin C (CCNC), and oncogenes including malignant fibrous histiocytoma amplified sequence 1 (MFHAS1/MASL1), high mobility group AT-hook 2 (HMGA2), PPAR binding protein (PPARBP), growth factor receptor-bound protein 7 (GRB7), and TBC1 (tre-2, BUB2, cdc16) domain family, member 1 (TBC1D1).
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1. College of Medicine (의과대학) > Dept. of Internal Medicine (내과학교실) > 1. Journal Papers
1. College of Medicine (의과대학) > Dept. of Pathology (병리학교실) > 1. Journal Papers
1. College of Medicine (의과대학) > Medical Research Center (임상의학연구센터) > 1. Journal Papers
5. Research Institutes (연구소) > Cancer Metastasis Research Center (암전이연구센터) > 1. Journal Papers
Yonsei Authors
Rha, Sun Young(라선영) ORCID logo https://orcid.org/0000-0002-2512-4531
Yang, Sang Hwa(양상화)
Yang, Woo Ick(양우익) ORCID logo https://orcid.org/0000-0002-6084-5019
Jeong, Ha Jin(정하진)
Chung, Hyun Cheol(정현철) ORCID logo https://orcid.org/0000-0002-0920-9471
Jeung, Hei Cheul(정희철) ORCID logo https://orcid.org/0000-0003-0952-3679
Choi, Yeon Ho(최연호)
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