Molecular basis of the differences between normal and tumor tissues of gastric cancer

Sanghwa Yang, Jihye Shin, Kyu Hyun Park, Hei Cheul Jeung, SunYoung Rha, Sung Hoon Noh, Woo Ick Yang, Hyuncheol Chung

Research output: Contribution to journalArticle

32 Citations (Scopus)

Abstract

To be able to describe the differences between the normal and tumor tissues of gastric cancer at a molecular level would be essential in the study of the disease. We investigated the gene expression pattern in the two types of tissues from gastric cancer by performing expression profiling of 86 tissues on 17K complementary DNA microarrays. To select for the differentially expressed genes, class prediction algorithm was employed. For predictor selection, samples were first divided into a training (n = 58), and a test set (n = 28). A group of 894 genes was selected by a t-test in a training set, which was used for cross-validation in the training set and class (normal or tumor) prediction in the test set. Smaller groups of 894 genes were individually tested for their ability to correctly predict the normal or tumor samples based on gene expression pattern. The expression ratios of the 5 genes chosen from microarray data can be validated by real time RT-PCR over 6 tissue samples, resulting in a high level of correlation, individually or combined. When a representative predictor set of 92 genes was examined, pathways of 'focal adhesion' (with gene components of THBS2, PDGFD, MAPK1, COL1A2, COL6A3), 'ECM-receptor interaction' pathway (THBS2, COL1A2, COL6A3, FN1) and 'TGF-beta signaling' (THBS2, MAPK1, INHBA) represent some of the main differences between normal and tumor of gastric cancer at a molecular level.

Original languageEnglish
Pages (from-to)1033-1040
Number of pages8
JournalBiochimica et Biophysica Acta - Molecular Basis of Disease
Volume1772
Issue number9
DOIs
Publication statusPublished - 2007 Sep 1

Fingerprint

Stomach Neoplasms
Genes
Neoplasms
Gene Components
Gene Expression
Focal Adhesions
Oligonucleotide Array Sequence Analysis
Transforming Growth Factor beta
Real-Time Polymerase Chain Reaction
Complementary DNA
alpha 2(I) collagen

All Science Journal Classification (ASJC) codes

  • Molecular Medicine
  • Molecular Biology

Cite this

Yang, Sanghwa ; Shin, Jihye ; Park, Kyu Hyun ; Jeung, Hei Cheul ; Rha, SunYoung ; Noh, Sung Hoon ; Yang, Woo Ick ; Chung, Hyuncheol. / Molecular basis of the differences between normal and tumor tissues of gastric cancer. In: Biochimica et Biophysica Acta - Molecular Basis of Disease. 2007 ; Vol. 1772, No. 9. pp. 1033-1040.
@article{4661a81dea204cc0a33293fb92ed0c4b,
title = "Molecular basis of the differences between normal and tumor tissues of gastric cancer",
abstract = "To be able to describe the differences between the normal and tumor tissues of gastric cancer at a molecular level would be essential in the study of the disease. We investigated the gene expression pattern in the two types of tissues from gastric cancer by performing expression profiling of 86 tissues on 17K complementary DNA microarrays. To select for the differentially expressed genes, class prediction algorithm was employed. For predictor selection, samples were first divided into a training (n = 58), and a test set (n = 28). A group of 894 genes was selected by a t-test in a training set, which was used for cross-validation in the training set and class (normal or tumor) prediction in the test set. Smaller groups of 894 genes were individually tested for their ability to correctly predict the normal or tumor samples based on gene expression pattern. The expression ratios of the 5 genes chosen from microarray data can be validated by real time RT-PCR over 6 tissue samples, resulting in a high level of correlation, individually or combined. When a representative predictor set of 92 genes was examined, pathways of 'focal adhesion' (with gene components of THBS2, PDGFD, MAPK1, COL1A2, COL6A3), 'ECM-receptor interaction' pathway (THBS2, COL1A2, COL6A3, FN1) and 'TGF-beta signaling' (THBS2, MAPK1, INHBA) represent some of the main differences between normal and tumor of gastric cancer at a molecular level.",
author = "Sanghwa Yang and Jihye Shin and Park, {Kyu Hyun} and Jeung, {Hei Cheul} and SunYoung Rha and Noh, {Sung Hoon} and Yang, {Woo Ick} and Hyuncheol Chung",
year = "2007",
month = "9",
day = "1",
doi = "10.1016/j.bbadis.2007.05.005",
language = "English",
volume = "1772",
pages = "1033--1040",
journal = "Biochimica et Biophysica Acta - Molecular Basis of Disease",
issn = "0925-4439",
publisher = "Elsevier",
number = "9",

}

Molecular basis of the differences between normal and tumor tissues of gastric cancer. / Yang, Sanghwa; Shin, Jihye; Park, Kyu Hyun; Jeung, Hei Cheul; Rha, SunYoung; Noh, Sung Hoon; Yang, Woo Ick; Chung, Hyuncheol.

In: Biochimica et Biophysica Acta - Molecular Basis of Disease, Vol. 1772, No. 9, 01.09.2007, p. 1033-1040.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Molecular basis of the differences between normal and tumor tissues of gastric cancer

AU - Yang, Sanghwa

AU - Shin, Jihye

AU - Park, Kyu Hyun

AU - Jeung, Hei Cheul

AU - Rha, SunYoung

AU - Noh, Sung Hoon

AU - Yang, Woo Ick

AU - Chung, Hyuncheol

PY - 2007/9/1

Y1 - 2007/9/1

N2 - To be able to describe the differences between the normal and tumor tissues of gastric cancer at a molecular level would be essential in the study of the disease. We investigated the gene expression pattern in the two types of tissues from gastric cancer by performing expression profiling of 86 tissues on 17K complementary DNA microarrays. To select for the differentially expressed genes, class prediction algorithm was employed. For predictor selection, samples were first divided into a training (n = 58), and a test set (n = 28). A group of 894 genes was selected by a t-test in a training set, which was used for cross-validation in the training set and class (normal or tumor) prediction in the test set. Smaller groups of 894 genes were individually tested for their ability to correctly predict the normal or tumor samples based on gene expression pattern. The expression ratios of the 5 genes chosen from microarray data can be validated by real time RT-PCR over 6 tissue samples, resulting in a high level of correlation, individually or combined. When a representative predictor set of 92 genes was examined, pathways of 'focal adhesion' (with gene components of THBS2, PDGFD, MAPK1, COL1A2, COL6A3), 'ECM-receptor interaction' pathway (THBS2, COL1A2, COL6A3, FN1) and 'TGF-beta signaling' (THBS2, MAPK1, INHBA) represent some of the main differences between normal and tumor of gastric cancer at a molecular level.

AB - To be able to describe the differences between the normal and tumor tissues of gastric cancer at a molecular level would be essential in the study of the disease. We investigated the gene expression pattern in the two types of tissues from gastric cancer by performing expression profiling of 86 tissues on 17K complementary DNA microarrays. To select for the differentially expressed genes, class prediction algorithm was employed. For predictor selection, samples were first divided into a training (n = 58), and a test set (n = 28). A group of 894 genes was selected by a t-test in a training set, which was used for cross-validation in the training set and class (normal or tumor) prediction in the test set. Smaller groups of 894 genes were individually tested for their ability to correctly predict the normal or tumor samples based on gene expression pattern. The expression ratios of the 5 genes chosen from microarray data can be validated by real time RT-PCR over 6 tissue samples, resulting in a high level of correlation, individually or combined. When a representative predictor set of 92 genes was examined, pathways of 'focal adhesion' (with gene components of THBS2, PDGFD, MAPK1, COL1A2, COL6A3), 'ECM-receptor interaction' pathway (THBS2, COL1A2, COL6A3, FN1) and 'TGF-beta signaling' (THBS2, MAPK1, INHBA) represent some of the main differences between normal and tumor of gastric cancer at a molecular level.

UR - http://www.scopus.com/inward/record.url?scp=34548160078&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=34548160078&partnerID=8YFLogxK

U2 - 10.1016/j.bbadis.2007.05.005

DO - 10.1016/j.bbadis.2007.05.005

M3 - Article

VL - 1772

SP - 1033

EP - 1040

JO - Biochimica et Biophysica Acta - Molecular Basis of Disease

JF - Biochimica et Biophysica Acta - Molecular Basis of Disease

SN - 0925-4439

IS - 9

ER -