定义:transcription factor binding site(TFBS) TFBS指的是TF特异结合的DNA分子的position(位置),延伸的话,就是DNA片段的序列边界。 注意,文献中经常把结合位点和结合域混淆(binding site ,binding motif) 我们推荐保留“site”这个词来定义某一特别sequence(基因的或artificial),这是一个factor结合的地方。而“motif”...
To verify whether DENIS identified a motif that can be attributed to the Dux factor, we used a previously published ChIP-seq for Dux19. The genome was scanned for binding sites, followed by binding site enrichment analysis of ChIP-peaks against the whole genome. We found the highest ...
Transcription factors are thought to regulate the transcription of microRNA genes in a manner similar to that of protein-coding genes; that is, by binding to conventional transcription factor binding site DNA sequences located in or near promoter regions that lie upstream of the microRNA genes. H...
Methods, Systems, and Media for Identifying Transcription Factor Binding SitesProvided are systems, methods, and media that receive chromosome sequence data; select a first plurality of overlapping octamers from the chromosome sequence data; assign an enrichment score to each of the first plurality of...
Here, we showed that the transcription factor PU.1 regulated gene expression in early T cell development both by recruiting partner transcription factors to its own binding sites and by depleting them from the binding sites that they preferred when PU.1 was absent. The removal of partner factors...
Nrf2 is a transcription factor belonging to a subfamily with a Cap “n” Collar (CNC) structure. It contains a basic leucine zipper DNA-binding domain identified in chicken beta-globin enhancer.1Subsequently, Nrf2 is widely present in all the human tissues where it acts as a transcription...
Initial computational approaches for genome-wide TSS identification focused on the use of sequence features such as over-represented k-mers, transcription factor binding site enrichment, conservation, and CpG content9,10,11,12,13. Such sequence-based strategies often lead to a large number of false...
Gene expression is to large degree regulated by the specific binding of protein transcription factors to cis-regulatory transcription factor binding sites in gene promoter regions. Despite the identification of hundreds of binding site sequence motifs, t
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
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,...