Mammalian Genome

, Volume 16, Issue 12, pp 942–954

Transcriptome analysis of human gastric cancer

Authors

  • Jung-Hwa Oh
    • Laboratory of Human GenomicsKorea Research Institute of Bioscience and Biotechnology (KRIBB)
  • Jin Ok Yang
    • National Genome Information Center (NGIC)Korea Research Institute of Bioscience and Biotechnology (KRIBB)
  • Yoonsoo Hahn
    • Laboratory of Human GenomicsKorea Research Institute of Bioscience and Biotechnology (KRIBB)
  • Mi-Rang Kim
    • Laboratory of Human GenomicsKorea Research Institute of Bioscience and Biotechnology (KRIBB)
  • Sang-Soon Byun
    • Laboratory of Human GenomicsKorea Research Institute of Bioscience and Biotechnology (KRIBB)
  • Yeo-Jin Jeon
    • Laboratory of Human GenomicsKorea Research Institute of Bioscience and Biotechnology (KRIBB)
  • Jeong-Min Kim
    • Laboratory of Human GenomicsKorea Research Institute of Bioscience and Biotechnology (KRIBB)
  • Kyu-Sang Song
    • College of MedicineChungNam National University
  • Seung-Moo Noh
    • College of MedicineChungNam National University
  • Sangsoo Kim
    • Department of Bioinformatics and Life ScienceSoongsil University
  • Hyang-Sook Yoo
    • Laboratory of Human GenomicsKorea Research Institute of Bioscience and Biotechnology (KRIBB)
  • Yong Sung Kim
    • Laboratory of Human GenomicsKorea Research Institute of Bioscience and Biotechnology (KRIBB)
    • Laboratory of Human GenomicsKorea Research Institute of Bioscience and Biotechnology (KRIBB)
Article

DOI: 10.1007/s00335-005-0075-2

Cite this article as:
Oh, J., Yang, J.O., Hahn, Y. et al. Mamm Genome (2005) 16: 942. doi:10.1007/s00335-005-0075-2

Abstract

To elucidate the genetic events associated with gastric cancer, 124,704 cDNA clones were collected from 37 human gastric cDNA libraries, including 20 full-length enriched cDNA libraries of gastric cancer cell lines and tissues from Korean patients. An analysis of the collected ESTs revealed that 97,930 high-quality ESTs coalesced into 13,001 clusters, of which 11,135 clusters (85.6%) were annotated to known ESTs. The analysis of the full-length cDNAs also revealed that 4862 clusters (51.7%) contained at least one putative full-length cDNA clone with an initiation codon, with the average length of the 5′ UTR of 140 bp. A large number appear to have a diverse transcription start site (TSS). An examination of the TSS of some genes, such as TEGT and GAPD, using 5′ RACE revealed that the predicted TSSs are actually found in human gastric cancer cells and that several TSSs differ depending on the specific gastric cell line. Furthermore, of the human gastric ESTs, 766 genes (9.5%) were present as putative alternatively spliced variants. Confirmation of the predicted spliced isoforms using RT-PCR showed that the predicted isoforms exist in gastric cancer cells and some isoforms coexist in gastric cell lines. These results provide potentially useful information for elucidating the molecular mechanisms associated with gastric oncogenesis.

Supplementary material

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Supplementary material

Copyright information

© Springer Science+Business Media, Inc. 2005