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

Sanghwa Yang, Hei Cheul Jeung, Ha Jin Jeong, Yeon Ho Choi, Ji Eun Kim, Jae Joon Jung, SunYoung Rha, Woo Ick Yang, Hyuncheol Chung

Research output: Contribution to journalArticle

42 Citations (Scopus)

Abstract

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).

Original languageEnglish
Pages (from-to)451-459
Number of pages9
JournalGenomics
Volume89
Issue number4
DOIs
Publication statusPublished - 2007 Apr 1

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DNA Copy Number Variations
Stomach Neoplasms
Gene Expression
Genes
Gene Expression Profiling
Oligonucleotide Array Sequence Analysis
GRB7 Adaptor Protein
Mediator Complex Subunit 1
Cyclin C
AT-Hook Motifs
Malignant Fibrous Histiocytoma
Neoplasms
Messenger RNA
Comparative Genomic Hybridization
Gene Dosage
Monoamine Oxidase
Fluorescence In Situ Hybridization
Oncogenes
Cluster Analysis
Real-Time Polymerase Chain Reaction

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

Yang, Sanghwa ; Jeung, Hei Cheul ; Jeong, Ha Jin ; Choi, Yeon Ho ; Kim, Ji Eun ; Jung, Jae Joon ; Rha, SunYoung ; Yang, Woo Ick ; Chung, Hyuncheol. / Identification of genes with correlated patterns of variations in DNA copy number and gene expression level in gastric cancer. In: Genomics. 2007 ; Vol. 89, No. 4. pp. 451-459.
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Identification of genes with correlated patterns of variations in DNA copy number and gene expression level in gastric cancer. / Yang, Sanghwa; Jeung, Hei Cheul; Jeong, Ha Jin; Choi, Yeon Ho; Kim, Ji Eun; Jung, Jae Joon; Rha, SunYoung; Yang, Woo Ick; Chung, Hyuncheol.

In: Genomics, Vol. 89, No. 4, 01.04.2007, p. 451-459.

Research output: Contribution to journalArticle

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