Transcriptome analysis of human gastric cancer.
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.
Oh
Jung-Hwa
JH
Laboratory of Human Genomics, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon , 305-333, Korea.
Yang
Jin Ok
JO
Hahn
Yoonsoo
Y
Kim
Mi-Rang
MR
Byun
Sang-Soon
SS
Jeon
Yeo-Jin
YJ
Kim
Jeong-Min
JM
Song
Kyu-Sang
KS
Noh
Seung-Moo
SM
Kim
Sangsoo
S
Yoo
Hyang-Sook
HS
Kim
Yong Sung
YS
Kim
Nam-Soon
NS
D020121:5' Untranslated Regions / Q000235:genetics; D017398:Alternative Splicing; D000595:Amino Acid Sequence; D019295:Computational Biology; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D015723:Gene Library; D006801:Humans; D008969:Molecular Sequence Data; D016415:Sequence Alignment; D012985:Software Design; D013274:Stomach Neoplasms / Q000235:genetics* / Q000378:metabolism; D024363:Transcription Initiation Site / Q000502:physiology*
D020121:5' Untranslated Regions