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...
Results of an in silico transcription factor binding motif analysis.Stefan WallnerMargot GrandlTatiana KonovalovaAlexander SigrünerThomas KopfMarkus PeerEvelyn OrsoGerhard LiebischGerd Schmitz
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。 scFAN...
BIOINFORMATICS APPLICATIONS NOTE Sequence analysis BEST: Binding-site Estimation Suite of Tools Dongsheng Che,Shane Jensen,Liming Cai,... - 《Bioinformatics》 - 2005 - 被引量: 76 Supervised Detection of Regulatory Motifs in ...
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 ...
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...
As a key transcription factor, using this new approach, we successfully determined the genome-wide distribution of GmJAG1-specific binding sites (GmJBSs), established a putative regulatory network centered on GmJAG1, and identified a novel GmJAG1-binding motif. Furthermore, we found that GmJBSs...
Here we report the 2.0 脜 resolution crystal structure of the bZIP motif of one such transcription factor, PAP1, a fission yeast AP-1-like ... Fujii,Yoshifumi,Shimizu,... - 《Nature Structural Biology》 被引量: 213发表: 2000年 A comparative analysis of transcription factor binding models ...
The conversion of DNA motif matrices into numerical matrices allows the use ofl Component Analysis (PCA) to model the binding sites which captures the information of the interdependences into the covariance, a second order statistics. Using the hypothesis that the binding sites will fit better to ...