National Tsing Hua University Institutional Repository:Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data
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    National Tsing Hua University Institutional Repository > 電機資訊學院 > 電機工程學系 > 期刊論文 >  Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data


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    题名: Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data
    作者: Wei-Sheng Wu
    Wen-Hsiung Li
    Bor-Sen Chen
    教師: 陳博現
    日期: 2007
    出版者: BioMed Central
    關聯: BMC BIOINFORMATICS   Volume: 8 Article Number: 188   Published: JUN 8 2007
    关键词: transcription factors
    TFs
    Temporal Relationship Identification Algorithm
    TRIA
    摘要: Background
    ChIP-chip data, which indicate binding of transcription factors (TFs) to DNA regions in vivo, are widely used to reconstruct transcriptional regulatory networks. However, the binding of a TF to a gene does not necessarily imply regulation. Thus, it is important to develop methods to identify regulatory targets of TFs from ChIP-chip data.
    Results
    We developed a method, called Temporal Relationship Identification Algorithm (TRIA), which uses gene expression data to identify a TF's regulatory targets among its binding targets inferred from ChIP-chip data. We applied TRIA to yeast cell cycle microarray data and identified many plausible regulatory targets of cell cycle TFs. We validated our predictions by checking the enrichments for functional annotation and known cell cycle genes. Moreover, we showed that TRIA performs better than two published methods (MA-Network and MFA). It is known that co-regulated genes may not be co-expressed. TRIA has the ability to identify subsets of highly co-expressed genes among the regulatory targets of a TF. Different functional roles are found for different subsets, indicating the diverse functions a TF could have. Finally, for a control, we showed that TRIA also performs well for cell-cycle irrelevant TFs.
    Conclusion
    Finding the regulatory targets of TFs is important for understanding how cells change their transcription program to adapt to environmental stimuli. Our algorithm TRIA is helpful for achieving this purpose.
    相関连結: http://www.biomedcentral.com/home/
    URI: http://nthur.lib.nthu.edu.tw/handle/987654321/12007
    显示于类别:[電機工程學系] 期刊論文
    [通訊工程研究所] 期刊論文

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