Transcriptome analysis of human gastric cancer.

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.

• Authors: Jung-Hwa Oh, Jin Ok Yang, Yoonsoo Hahn, Mi-Rang Kim, Sang-Soon Byun, Yeo-Jin Jeon, Jeong-Min Kim, Kyu-Sang Song, Seung-Moo Noh, Sangsoo Kim, Hyang-Sook Yoo, Yong Sung Kim, Nam-Soon Kim
• Journal: Mammalian genome : official journal of the International Mammalian Genome Society (Mamm Genome) Vol. 16 Issue 12 Pg. 942-54 (Dec 2005) ISSN: 0938-8990 [Print] United States
• PMID: 16341674 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)

Chemical References

• 5' Untranslated Regions

Topics

• 5' Untranslated Regions (genetics)
• Alternative Splicing
• Amino Acid Sequence
• Computational Biology
• Expressed Sequence Tags
• Gene Expression Profiling
• Gene Expression Regulation, Neoplastic
• Gene Library
• Humans
• Molecular Sequence Data
• Sequence Alignment
• Software Design
• Stomach Neoplasms (genetics, metabolism)
• Transcription Initiation Site (physiology)