Homology Comparison of the cDNA Sequences in Vertebrates for Screening the Commonly Expressed Genes with Related Functions during Early Embryonic Stages
Date Issued
2007
Date
2007
Author(s)
Lien, Ching-Yi
DOI
zh-TW
Abstract
The early embryonic stages of mammals are the developmental process from zygote to preimplantation. The stages of embryogenesis are critical for embryonic development in vertebrates. Several key developmental events occurr in these stages, such as cell growth, migration, differentiation, and morphogenesis. In spite of the importance occurring in the early embryogenesis, limited information has been provided by previous studies. For this reason, the purpose of this study is to utilize the public databases to screen those commonly expressed genes with their related functions at early embryonic stages in vertebrates.
The UniGene and the Gene Index databases in the National Center for Biotechnology Information (NCBI) and The Institute for Genomic Research (TIGR) were designed to collect and assemble sequences of expressed sequences tags (ESTs) and mRNA. Each assembled entry is a set of transcript sequences that appear to come from the same transcription locus. The numbers of unigene entries and tentative consensuses (TC) of embryos before implantation collected from Bos taurus (Bt), Mus musculus (Mm), Sus scrofa (Ssc) and Xenopus laevis (Xl) were 2,407, 13,705, 4,015, and 15,329, respectively. The analytic results among four species were divided into seven groups. All of the commonly expressed genes were 1,414 for Mm and Bt; 1,909 for Mm and Ssc; 2,372 for Mm and Xl; 411 for Mm, Bt and Ssc; 602 for Mm, Bt and Xl and 860 for Mm, Ssc and Xl. However, there were 254 genes commonly expressed in all these four species. Furthermore, the unigenes of Mm were classified according to the Gene Ontology (GO) by three categories: biological process (P), molecular function (F) and cellular component (C). The results among Mm, Bt, Ssc and Xl showed the entries with GO identifiers were 112 (P), 113 (F) and 105 (C); the results between Mm and Ssc showed the entries with GO identifiers were 857 (P), 926 (F) and 862 (C); the results between Mm and Xl showed the entries with GO identifiers were 1,208 (P), 1,281 (F) and 1,145 (C). For the entries that mapped to biological processes, most of them with their functional annotations were related to metabolic processes. For molecular function, most of the commonly expressed genes were related to some macromolecule or ion binding. In addition, these activated genes are expressed intracellularly at early developmental stages.
The commonly expressed genes and their related functions might be annotated using comparison tool among sequence databases of different species. The analytical procedure would assist animal scientists to screen the conserved genes with fundamental roles and functions.
Subjects
共同表現基因
早期胚發育
功能性解析
脊椎動物
Commonly expressed genes
Early embryonic development
Functional annotation
Vertebrates
Type
thesis
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