Transcription factor binding site analysis.Jörg BartelJan KrumsiekKatharina SchrammJerzy AdamskiChristian GiegerChristian HerderMaren CarstensenAnnette PetersWolfgang RathmannMichael Roden
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...
2007. Analysis of transcription factor HY5 genomic binding sites revealed its hierarchical role in light regulation of development. The Plant Cell 19, 731-... Lee J,He K,Stolc V,... - 《Plant Cell》 被引量: 0发表: 2007年 Embryonic Stem Cell-Specific miR302-367 Cluster: Human Gene Stru...
研究也可以做得很深,了解一个物种里面有哪些transcription factor families,这些转录因子各自是如何发挥作用的,这些家族是如何归类的,各自有什么特性。 TRANSCRIPTION FACTORS: Structural Families and Principles of DNA Recognition【非常古老的综述1992年,也非常有意思,涉及了TF binding的本质,而不是浮在表面】 Arabidopsi...
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...
Transcription factor binding site orientation and order are major drivers of gene regulatory activity Ilias Georgakopoulos-Soares, Chengyu Deng, Vikram Agarwal, Candace S. Y. Chan, Jingjing Zhao, Fumitaka Inoue & Nadav Ahituv Nature Communications volume 14, Article number: 2333 (2023) ...
A prerequisite for successful promoter analysis is the predi... K Cartharius,K Frech,K Grote,... - 《Bioinformatics》 被引量: 3508发表: 2005年 Similarity of position frequency matrices for transcription factor binding sites Transcription-factor binding sites (TFBS) in promoter sequences of ...
Unbound transcription factor is then removed or washed from the solid substrate and labelled, sequence-specifically bound transcription factor is detected. Incubates which include candidate agents which alter transcription factor binding deviate from control incubates in terms of label signal--typically, ...
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 ...
【文献报告】Mammalian evolution of human cis-regulatory elements and transcription factor binding sites 该研究旨在通过对241个哺乳动物基因组的参考无序比对,绘制0.92百万个人类候选顺式调控元件(cCREs)和15.6百万个人类转录因子结合位点(TFBSs)的进化轨迹。研究发现,有439,461个cCREs和2,024,062个TFBSs处于进化...