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”这个词进行结合特异性的genetic(遗传学的)描述,通过汇总一系列sites的信息进行汇总得到。 定义:TFBM (transcription factor binding motif) 转录因子结合域 “代表一个TF的结合特异性,通常通过汇总一系列结合...
This clustering model is implemented, using a Gibbs sampling\nstrategy, on several collections of transcription factor motif matrices. Our\nclusters provide a means by which to organize transcription factors based on\nbinding motif similarities, which can be used to reduce motif redundancy within\n...
In some dimeric cases of transcription factor (TF) binding, the specificity of dimeric motifs has been observed to differ notably from what would be expected were the two factors to bind to DNA independently of each other. Current motif discovery methods are unable to learn monomeric and dimeric...
Transcription factor binding site maps Position frequency matrices (PFMs) of transcription factors were derived from JASPAR (release 2022) for the non-redundant CORE vertebrate collection (http://jaspar.genereg.net/download/CORE/JASPAR2022_CORE_vertebrates_non-redundant_pfms_meme.zip)20 and motif scan...
本文提介绍了scFAN(single-cell factor analysis network单细胞因子分析网络),这是一种深度学习模型,可以预测单个细胞中全基因组的转录因子结合网络。 scFAN包括对大量的数据进行“预训练模型”训练,然后使用DNA序列数据,汇总的相似scATAC-seq数据和可定位性数据的组合,将其用于预测单细胞水平上的转录因子结合。
A sequence motif is a short recurring pattern with biological significance such as a DNA-recognition sequence for a transcription factor (TF), an mRNA splicing signal, or a functional region of a protein domain. Many high-throughput experimental approaches and computational tools have been developed...
CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments. Bioinformatics. 2011;27(5):715-7.Kuttippurathu L, Hsing M, Liu ... SW Kong - 《Bioinformatics》 被引量: 77发表: 2011...
In summary, we present a new computational toolkit, MAmotif, for detecting co-factors associated with the differential chromatin binding of proteins, based on quantitative comparison of their ChIP-seq data and systematic integration with TF binding information from motif analysis or other resources. Ap...
DNA-dependent formation of transcription factor pairs alters their 552 binding specificity【Nature丨转录因子结合核小体的五种方式(全景图)】 总而言之,DNA打包到核小体上,会使转录因子更难接近DNA。而这项研究向我们展示了转录因子在困难面前,通过其他多种形式接近核小体上的DNA,获取基因组中的重要信息,控制细...
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 enrichment for motif 20, which is a motif ...