Transcription factor binding sitesConvolutional neural networksMotif discoveryBioinformaticsAutoencoderTranscription factor binding site (TFBS) is a DNA sequence that binds to transcription factor and regulates
Recently, deep learning based models have been proposed and have shown competitive results on a transcription factor binding site prediction task. However, it is difficult to interpret the prediction results obtained from the previous models. In addition, the previous models assumed all the sequence ...
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 ...
Several transcription factors have been discovered that have a DNA binding motif that is also present in the HMG proteins. Designated the HMG box, this sequence is present in the eukaryotic upstream binding factor (UBF) (Jantzen et al., 1990), in mitochondrial transcription factor 1 (Parisi...
I. (2014) Application of experimentally verified transcription factor binding sites models for computational analysis of ChIP-Seq data. BMC Genomics 15, 80.Levitsky VG, Kulakovskiy IV, Ershov NI, Oschepkov DY, Makeev VJ, Hodgman TC, 11 Merkulova TI: Application of experimentally verified ...
MDP was developedusing a TF distribution pattern curve generated by analyzing 25 yeast TFs and37 of their experimentally validated binding motifs, followed by calculatinga scoring value to quantify the reliability of each motif prediction. Finally,MDP was tested using another set of 7 TFs with ...
Kim NK, Tharakaraman K, Marino-Ramirez L, Spouge JL (2008) Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites. BMC Bioinformatics 9: 262.Kim NK, Tharakaraman K, Marino-Ramirez L, Spouge JL. Finding sequence motifs...
sequencing adapters into accessible chromatin, enabling mapping of regulatory regions across the genome. Additionally, the local distribution of Tn5 insertions contains information about transcription factor binding due to the visible depletion of insertions around sites bound by protein - known asfootprints...
Omni-ATAC-seq and DNase-seq are equivalent in the prediction of cell-specific transcription factor binding There is a perception in the field that DNase-seq libraries are superior to ATAC-seq for computational footprinting [11,15]. To address this, we compare the predictive performance of HINT-...
Transcription factor binding site TSS: Transcription start site UCSC: University of California Santa Cruz References Valen E, Krogh A, Hayashizaki Y, Carninci P. A code for transcription initiation in mammalian genomes. Genome Res. 2008;18:1–12. Article Google Scholar FANTOM Consortium and...