Most proposed methods for TF-binding site (TFBS) predictions only use low order dependencies for predictions due to the lack of efficient methods to extract higher order dependencies. In this work, We first propose a novel method to extract higher order dependencies by applying CNN on histone mod...
Prediction of TF target sites based on atomistic models of protein-DNA complexes. BMC Bioinformatics. 2008; 9 :436.V. Angarica, A. Perez, A. Vasconcelos, J. Collado-Vides, and B. Contreras-Moreira, "Prediction of tf target sites based on atomistic models of protein-dna complexes," BMC ...
We calculated the area under the precision-recall curve at a false discovery rate cutoff of 0.5 for the LR-DNase model, a number of logistic regression models with fewer features, and several existing state-of-the-art TF binding prediction methods. The LR-DNase model outperformed existing ...
TFBert: Improving language model of human genome for DNA–protein binding prediction based on task-specific pre-training - lhy0322/TFBert
Information on specific combinations of transcription factor binding sites on user submitted sequences also needs to be extracted, as it strengthens the prediction for a sequence being real or background. Implementation The web front-end is programmed in PHP (v4.3) [2] running on an Apache WWW...
e, DeepHeam ChIP-seq binding prediction score for CEBPB in lung fibroblast (IMR-90), alveolar basal epithelial adenocarcinoma (A549), the erythroleukaemia line (K562), human endothelial kidney cells (HEK293), and the GM12878 lymphoblastoid cell line (LCL) predicts increased binding to the risk...
[12]. The abundance of TFs for a given gene or the number of transcription-factor binding sites within its promoter or enhancer can affect the amplitude, periodicity, and duration of transcriptional bursts [15]. In addition, the nucleosome positions and activities of chromatin remodelers can also...
Before β-TrCP binding, the S393 and S397 residues in DSGXXS need to be phosphorylated. To search for candidate kinases, we used the Human Protein Reference Database and NetPhos 3.1 Server, another kinase prediction program (Blom et al., 2004), and discovered that the S393 and S397 resi...
TFL1, on the other hand, is suggested to act as a floral repressor, competing with FT for binding to FD and 14-3-3 proteins, thus leading to the formation of a ‘floral-repressor complex’ that suppresses the floral transition [29,30,31]. Indeed, in line with this proposed model, a...
3′UTR-WT (Fig.6E), but the specific binding sites of each member in miR-16 family were not in full accord (Fig.6F). It has been reported diverse tumors possess downregulated miR-16 family, indicting possibly tumor suppressive capability. We investigated miR-16 family expression in LUAD ...