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KMID : 0811720040080000199
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Korean Journal of Physiology & Pharmacology
2004 Volume.8 No. 0 p.199 ~ p.0
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Analysis of Gene Expression Profiles and Promoter Sequence Data for Reconstructing Regulatory Genetic Network
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Kim Min-Jung
Kim Hye-Young
Kim Hyo-Chang
Choi Min-Ee
Lee Seo-Eun
Shin Hong-Kee
Kim Jin-Hyuk
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Abstract
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The regulatory genetic network is the important mechanism underlying the function of the cell such as differentiation. At the beginning of understanding the whole regulatory genetic network related to a physiological phenotype, it is feasible to reconstruct the sub-network rather than the large- scale network. Therefore, it is critical to estimate genes which are the components of sub-networks from genome-wide data. We estimated genes for reconstructing sub-networks by analyzing gene expression profiles and promoter sequence data. The gene expression profiles were originated from cDNA microarray experiments which were performed at each developmental stage of mouse embryonic stem cells differentiated to neurons. The gene expression data at each stage were obtained from the triplicated microarray experiments. Besides, promoter sequence data were selected upstream ORF sequences from NCBI database. Clustered genes were acquired by applying SVD and k-mean algorithms to the analysis of gene expression profiles. In each group of clustered genes, the consensus sequences were obtained through processing promoter sequences with MEME. Moreover, the functional properties of these motifs were validated by using TRANSFAC. We suggest that these results are able to provide the fundamental information and materials for reconstructing regulatory genetic network.
Source: Korean Journal of Physiology & Pharmacology.2004 Oct;8(Suppl I):S144-S144
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KEYWORD
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Genetic network, Motif, Gene expression
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