The transcription factor affinity prediction (TRAP) method calculates the affinity of transcription factors for DNA sequences on the basis of a biophysical model. This method has proven to be useful for several applications, including for determining the putative target genes of a given factor. This...
In computational methods, position weight matrices (PWMs) are commonly applied for transcription factor binding site (TFBS) prediction. Although these matrices are more accurate than simple consensus sequences to predict actual binding sites, they usually produce a large number of false positive (FP)...
Here, we developed a novel orientation-dependent, knowledge-based, residue-level potential for improving transcription factor (TF)-DNA docking.Results: We demonstrated the performance of this new potential in TF-DNA binding affinity prediction, discrimination of native protein-DNA complex from decoy ...
transcription initiation A transcription factor affinity-based code for mammalian Material Supplemental M Megraw,FC Pereira,ST Jensen,... 被引量: 0发表: 2009年 Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity. Understanding the regulation of human ...
Khamis AM, Motwalli O, Oliva R, Jankovic BR, Medvedeva YA, Ashoor H, Essack M, Gao X and Bajic VB: A novel method for improved accuracy of transcription factor binding site prediction. Nucleic Acids Res. 46(e72)2018.PubMed/NCBIView Article:Google Scholar ...
BMO transcription factor binding prediction BMO (“Bee” MOdel of TF binding) builds on previous reports that the degree of chromatin accessibility around a motif15,16,17 and the presence of co-occurring motifs18 positively correlate with TF occupancy, corresponding to the analogy of TFs behaving ...
Experimental methods provide in vivo evidence of TF binding or in vitro measurement of affinity of TF–DNA interactions. However, large-scale and precise prediction of TFBSs remains one of the greatest challenges due to high cost and low time efficiency. Genome-wide TFBS identification thus ...
and C. Synteny analysis indicates that the firsts 3R-MYB gene was amplified through segmental duplications in Amborella. Gene duplications within these lineages after the separation of monocots and dicots are the important factor that explains the large diversity seen today. The general gene structure...
The optimized compounds had more affinity for their target, inhibited androgen-receptor-dependent transcriptional programs, and had an antitumorigenic effect in models of castration-resistant prostate cancer in cells and in vivo. These results suggest that it is possible to rationally optimize, and ...
Utilizing consecutive affinity-purification systematic evolution of ligands by exponential enrichment (CAP-SELEX) experiments, 9,400 transcription factor-transcription factor–DNA interactions were functionally analyzed showing that both the orientation and distance between TFBSs determined heterodimer formation ...