Here, using a massively parallel reporter assay (MPRA) of 209,440 sequences, we examine all possible pair and triplet combinations, permutations and orientations of eighteen liver-associated transcription factor binding sites (TFBS). We find that TFBS orientation and order have a major effect on ...
Therefore, a good database for plant TFs and transcription factor binding sites (TFBSs) will be useful for starting a series of complex experiments. In this chapter, PlantPAN (version 3.0) is utilized as an example to explain how bioinformatics systems advance research on gene regulation....
网络转录因子结合位点 网络释义 1. 转录因子结合位点 鉴定调控序列的转录因子结合位点(Transcription Factor Binding Sites)。预测“转录因子-靶基因”转录调控关系,在此基础上 … www.biosino.com.cn|基于6个网页 例句 释义: 全部,转录因子结合位点
Context-dependent transcription factor (TF) binding is one reason for differences in gene expression patterns between different cellular states. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) identifies genome-wide TF binding sites for one particular context—the cells used ...
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...
We present an all-atom molecular modeling method that can predict the binding specificity of a transcription factor based on its 3D structure, with no further information required. We use molecular dynamics and free energy calculations to compute the relative binding free energies for a transcription...
tompa m, li n, bailey tl, church gm, de moor b, eskin e, et al. assessing computational tools for the discovery of transcription factor binding sites. nat biotechnol. 2005;23(1):137–44. article cas pubmed google scholar luehr s, hartmann h, soding j. the xx...
Binding of transcription factors to transcription factor binding sites (TFBSs) is key to the mediation of transcriptional regulation. Information on experimentally validated functional TFBSs is limited and consequently there is a need for accurate predic
nerve factor-ß TFs: Transcription factors TFBSs: TF binding sites TSSs: transcription start sites PTEN : phosphatase and tensin homolog deleted on chromosome 10 LOH: loss of heterozygosity VDR : vitamin D receptor FISH: Fluorescent In Situ Hybridization ORI: over-representation index ...
Transposase-Accessible Chromatin followed by sequencing (ATAC-seq) is a simple protocol for detection of open chromatin. Computational footprinting, the search for regions with depletion of cleavage events due to transcription factor binding, is poorly u