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Please use this identifier to cite or link to this item: http://ntour.ntou.edu.tw:8080/ir/handle/987654321/46767

Title: De novo motif discovery facilitates identification of interactions between transcription factors in Saccharomyces cerevisiae
Authors: Mei-Ju May Chen
Lih-Ching Chou
Tsung-Ting Hsieh
Ding-Dar Lee
Kai-Wei Liu
Chi-Yuan Yu
Yen-Jen Oyang
Huai-Kuang Tsai
Chien-Yu Chen
Contributors: 國立臺灣海洋大學:資訊工程學系
NTOU:Department of Computer Science and Engineering
Date: 2012-01
Issue Date: 2018-06-04T08:25:27Z
Publisher: Bioinformatics
Abstract: Abstract:
Motivation: Gene regulation involves complicated mechanisms such as cooperativity between a set of transcription factors (TFs). Previous studies have used target genes shared by two TFs as a clue to infer TF–TF interactions. However, this task remains challenging because the target genes with low binding affinity are frequently omitted by experimental data, especially when a single strict threshold is employed. This article aims at improving the accuracy of inferring TF–TF interactions by incorporating motif discovery as a fundamental step when detecting overlapping targets of TFs based on ChIP-chip data.

Results: The proposed method, simTFBS, outperforms three naïve methods that adopt fixed thresholds when inferring TF–TF interactions based on ChIP-chip data. In addition, simTFBS is compared with two advanced methods and demonstrates its advantages in predicting TF–TF interactions. By comparing simTFBS with predictions based on the set of available annotated yeast TF binding motifs, we demonstrate that the good performance of simTFBS is indeed coming from the additional motifs found by the proposed procedures.

Contact:hktsai@iis.sinica.edu.tw; chienyuchen@ntu.edu.tw

Supplementary information:Supplementary data are available at Bioinformatics online.
Relation: 28(5), pp.701-708
URI: http://ntour.ntou.edu.tw:8080/ir/handle/987654321/46767
Appears in Collections:[資訊工程學系] 期刊論文

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