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|Title: ||Cross-species Functional Conservation and in silico Gene Replacement for HIF Pathways|
|Authors: ||Chia-Sheng Chuang;Chih-Chia Chen;Tun-Wen Pai;Chin-Hua Hu;Hao-Teng Chang;Margaret Dah-Tsyr Chang|
|Contributors: ||NTOU:Department of Computer Science and Engineering|
|Keywords: ||HIF (Hypoxia-inducible factor);KEGG (Kyoto Encyclopedia of Genes and Genomes);Orthology;Paralogy;Signaling pathway|
|Issue Date: ||2011-10-21T02:35:18Z
|Publisher: ||The Fourth International Conference on Computational Systems Biology (ISB2010)|
|Abstract: ||Abstract:Hypoxia-inducible factors (HIFs) are transcription factors that play a crucial role
in adaptive processes to a hypoxic cellular environment for most of organisms. The activation of HIF pathway has significant impacts on gene expression patterns in cancer research and it is important to analyze functional conservation and possible gene replacement within the HIF pathway for cancer therapies. Phylogenomics is a useful tool to identify the relationship among various species. By evaluating the evidence of homologous relationship within cross-species pathways, functional conservation and gene replacement for a specific biological function can be obtained. Mapping orthologous and paralogous genes through a phylogenetic tree onto the conserved pathways indicates a strong homology of function. This study retrieved an initial pathway from the KEGG pathway database, and constructed an ontology table through cross-species comparison. A quantitatively measured HIF pathway was depicted to illustrate suitable simulations of cellular function, and the built-up map discovered all substitutable genes and explored unknown subpathways by employing homologous appearing rates. Novel terminologies of OrthRate and ParaRate are proposed to quantitatively indicate the flexibility of a homologous pathway and to enhance the substitutable possibilities of functional genes. This is the first novel system which can generate homologous biological pathways for various organisms based on orthologous and paralogous gene analyses.
|Appears in Collections:||[資訊工程學系] 演講及研討會|
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