Renewal and preliminary study of expressed sequence tags database on human fetal liver aged 22 wk of gestation

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• 作者：TingGui Chen (1) (2)
  SongFeng Wu (1)
  GangQiao Zhou (1)
  YunPing Zhu (1)
  FuChu He (1)
  
• 关键词：human fetal liver ; expressed sequence tags ; cluster and assembly ; gene ontology ; hierarchical clustering
• 刊名：Chinese Science Bulletin
• 出版年：2008
• 出版时间：October 2008
• 年：2008
• 卷：53
• 期：20
• 页码：3204-3210
• 全文大小：480KB
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• 作者单位：TingGui Chen (1) (2)
  SongFeng Wu (1)
  GangQiao Zhou (1)
  YunPing Zhu (1)
  FuChu He (1)
  
  1. State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, 102206, China
  2. Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, China
  
• ISSN：1861-9541

文摘

With the developments of international human transcriptome data and our ESTs of human fetal liver aged 22 weeks (wk) of gestation (HFL22w), the former research must be renewed. In this work, the EST data were firstly clustered by blasting against the ESTs of HFL22w, UniGene, DoTS, MGC and Twinscan-predicted human transcriptome. Then, after EST assembly and gene identification, the known genes were classified by GO (gene ontology), and the unknown genes were predicted by Pfam and ScanProsite to clarify their functions. In the end, the relations of 5 tissues including fetal liver, adult liver, bone marrow, thymus and lymph node that possess hemopoiesis or can indicate fetal liver characteristics were analyzed by hierarchical clustering. The results show that: (i) By comparing the 5 newest human transcriptome databases, we can largely reduce the probability that the ESTs belonging to unconnected parts of one gene were probably divided into different clusters, so it is recommended to blast against the newest databases when clustering EST data; (ii) some previous unknown ESTs had been identified as function-known genes, and 1379 genes were identified as fully new sequences possessed in our lab; (iii) through GO classification, we got a rough understanding of HFL22w, and obtained 6 cell migration genes and 6 hemopoiesis genes; (iv) prediction of gene function had enabled us to obtain 277 profiles, among them, there are 5 categories distributed in more than 10 genes; (v) five tissue relations analyzed by hierarchical clustering are related to their functions; (vi) We have built the world’s largest EST database on HFL22w. Renewal and preliminary analysis of EST database on HFL22w will help to understand hemopoiesis and cell migration mechanism, and promote future research on human fetal liver.