Predicting enhancer-promoter interaction from genomic sequence with deep neural networks. bioRxiv, page 085241, 2016.Singh, S., Y. Yang, B. Poczos, and J. Ma, 2018 Predicting enhancer- promoter interaction from genomic sequence with deep neural networks. bioRxiv .Shashank Singh, Yang Yang, ...
BMC Bioinformatics (2024) 25:216 https://doi.org/10.1186/s12859-024-05784-9 BMC Bioinformatics RESEARCH Open Access EPI‑Trans: an effective transformer‑based deep learning model for enhancer promoter interaction prediction Fatma S. Ahmed1,2*, Saleh Aly2,3* and Xiangrong ...
5a). Contrary to the prediction from the two-state model46, each promoter exhibited a wide distribution with more than one population of active loci characterized by different expression levels (Fig. 5a). A natural explanation of this phenomenon is that some of the observed promoter loci may ...
Background: The enhancer–promoter interaction (EPI) is a critical component of gene regulatory networks, playing a significant role in understanding the complexity of gene expression. Traditional EPI prediction methods focus on one-to-one interactions, neglecting more complex one-to-many and many-to...
Here, we present PSYCHIC, a computational approach for analyzing Hi-C data and identifying promoter–enhancer interactions. We use a unified probabilistic model to segment the genome into domains, which we then merge hierarchically and fit using a local background model, allowing us to identify ...
We used an approach similar to calling SIP [55] to annotate loop-mediated genes in each breed. For each active promoter, we calculated the cumulative interaction score, defined as the sum of −log10FDR for interaction intensity. We then performed quantile–quantile normalization under the assump...
Since promoter elements are critical determinants of expression noise in bacteria and lower eukaryotic cells (Carey et al., 2013, Murphy et al., 2010), we reasoned that CTCF-mediated enhancer-promoter interaction may contribute to the control of expression noise and help to reduce cell-to-cell ...
Coronary artery disease (CAD) is a multifactorial disorder, which is partly heritable. Herein, we implemented a mapping of CAD-associated candidate genes by using genome-wide enhancer-promoter conformation (H3K27ac-HiChIP) and expression quantitative tra
were up-regulated by recurrent SEs, thereby maintaining GSC properties and promoting the malignancy of glioblastoma [154]. Consistently, the formation of new SE-promoter interaction regulated the expression of stemness-related CD276 in GSC [155]. Oncogenic TF KLF5 was correlated with the stemness ...
Sox5-mediated interaction between a novel enhancer and RORγt gene promoter promotes the RORγt gene expression and Th17 differentiation 喜欢 0 阅读量: 10 作者:Chao H.,Zhiyuan W.,Hui D.,Yuzhang W.,Yi T. 摘要: <正>Th17 cells play a critical role in the pathogenesis of inflammatory and...