Meta- and gene set analysis of stomach cancer gene expression data.
We generated gene expression data from the tissues of 50 gastric cancer patients, and applied meta-analysis and gene set analysis to this data and three other stomach cancer gene expression data sets to define the gene expression changes in gastric tumors. By meta-analysis we identified genes consistently changed in gastric carcinomas, while gene set analysis revealed consistently changed biological themes. Genes and gene sets involved in digestion, fatty acid metabolism, and ion transport were consistently down-regulated in gastric carcinomas, while those involved in cellular proliferation, cell cycle, and DNA replication were consistently up-regulated. We also found significant differences between the genes and gene sets expressed in diffuse and intestinal type gastric carcinoma. By gene set analysis of cytogenetic bands, we identified many chromosomal regions with possible gross chromosomal changes (amplifications or deletions). Similar analysis of transcription factor binding sites (TFBSs), revealed transcription factors that may have caused the observed gene expression changes in gastric carcinomas, and we confirmed the overexpression of one of these, E2F1, in many gastric carcinomas by tissue array and immunohistochemistry. We have incorporated the results of our meta- and gene set analyses into a web accessible database (http://human-genome.kribb.re.kr/stomach/).
Kim
Seon-Young
SY
Human Genomics Laboratory, Genome Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea.
Kim
Jeong-Hwan
JH
Lee
Heun-Sik
HS
Noh
Seung-Moo
SM
Song
Kyu-Sang
KS
Cho
June-Sik
JS
Jeong
Hyun-Yong
HY
Kim
Woo Ho
WH
Yeom
Young-Il
YI
Kim
Nam-Soon
NS
Kim
Sangsoo
S
Yoo
Hyang-Sook
HS
Kim
Yong Sung
YS
D001665:Binding Sites; D002869:Chromosome Aberrations; D030541:Databases, Genetic; D050687:E2F1 Transcription Factor / Q000378:metabolism; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D052138:Genes, Neoplasm; D006801:Humans; D046228:Microarray Analysis; D013274:Stomach Neoplasms / Q000235:genetics* / Q000473:pathology; D014157:Transcription Factors / Q000378:metabolism; D015854:Up-Regulation / Q000235:genetics
D050687:E2F1 Transcription Factor; D014157:Transcription Factors