In this paper, we propose an algorithm of predicting TF binding sites from a given set of sequences of upstream regions of genes using suffix array and local alignment algorithm. Our algorithm based on following two assumptions: i) there tends to be a common TF that binds with each of the...
Recently, deep learning based models have been proposed and have shown competitive results on a transcription factor binding site prediction task. However, it is difficult to interpret the prediction results obtained from the previous models. In addition, the previous models assumed all the sequence ...
Usually, transcription factor binding sites prediction methods based on PWMs require user-defined thresholds. The arbitrary threshold and also the relatively ... J Zheng,J Wu,Z Sun - 《Nucleic Acids Research》 被引量: 96发表: 2003年 Integrating genomic data to predict transcription factor binding...
Studies of gene regulation often utilize genome-wide predictions of transcription factor (TF) binding sites. Most existing prediction methods are based on sequence information alone, ignoring biological contexts such as developmental stages and tissue types. Experimental methods to study in vivo binding,...
The binding of transcription factors to specific locations in the genome is integral to the orchestration of transcriptional regulation in cells. To characterize transcription factor binding site function on a large scale, we predicted and mutagenized 45
Estimation of bound/unbound transcription factor binding sites Visualization of footprints within and across different conditions For information on each tool, please see thewiki. TOBIAS is written as a python package and can be quickly installed via pip: ...
Characterization of this region showed a multi-transcription factor binding arrangement that led to the identification of a potential role for the HAP2/3/5 complex in cellulase regulation, as well as possible binding sites for XYR1 and ACE2 (Zeilinger et al., 1998, 2001). In S. cerevisiae...
The ability to identify transcription factor binding sites(TFBSs) is necessary to understand gene regulation and infer regulatory networks.Despite the fact that bioinformatics tools have been developed for years toimprove computational identification of TFBSs, the accurate prediction stillremains changeling ...
Some of the “missing” overlap could perhaps be explained by alternative transcription factor binding sites, where a binding site active in only one cell type could have another nearby site active in the other cell type. To test this possibility, we counted the number of overlaps when allowing...
The TFSEARCH server predicted a variety of transcription factor-binding sites in the 5'-flanking region of the abLysG gene, some of which are involved ... SDNK Bathige,N Umasuthan,I Whang,... - 《Fish & Shellfish Immunology》 被引量: 29发表: 2013年 Negative regulation of cyclin D3 ...