ATAC-seq footprinting unravels kinetics of transcription
Aug 26, 2020 · In this investigation, we apply TOBIAS to ATAC-seq data from both human and mouse PD and show how visible TF footprints correlate with the timings of TF activity …
Uncovering uncharacterized binding of transcription factors from ATAC …
Apr 23, 2024 · Transcription factors (TFs) are crucial epigenetic regulators, which enable cells to dynamically adjust gene expression in response to environmental signals. Computational …
maxATAC: Genome-scale transcription-factor binding prediction from ATAC ...
Jan 31, 2023 · We first compared maxATAC model performance to the most popular method of TFBS prediction, TF motif scanning in ATAC-seq peaks [35–38] (implementation described in …
GNNMF: a multi-view graph neural network for ATAC-seq motif …
Mar 21, 2024 · Finding multiple ATAC-seq motifs. ATAC-seq can reveal all opening chromatin, which means that there are multiple motifs in an ATAC-seq dataset. In this study, we …
MMGAT: a graph attention network framework for ATAC-seq motifs …
Apr 20, 2024 · Motif finding in Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) data is essential to reveal the intricacies of transcription factor binding sites …
Transcription Factor Footprinting — Epigenomics Workshop 2024 …
In this tutorial we use an R / Bioconductor packages ATACseqQC and MotifDb to detect TF binding signatures in ATAC-seq data. Please note this tutorial is merely an early attempt to …
Identification of transcription factor binding sites using ATAC-seq
Feb 26, 2019 · We also evaluate motifs supported by Wellington footprints or motifs inside ATAC-seq peaks Footnote 4. We observe a number of TFs with statistically significant difference in …
Detecting Differential Transcription Factor Activity from ATAC …
Using public ATAC-seq data from a variety of human and mouse cell lines (IMR90, H524, NJH29, and BRG1 fl/fl) and perturbations (nutlin, doxycycline, and tamoxifen), we assessed changes …
ATAC-seq footprinting unravels kinetics of transcription factor …
Aug 26, 2020 · TOBIAS is a collection of command-line tools utilizing a minimal input of ATAC-seq reads, TF motifs and genome information (Fig. 1b) to perform all levels of footprinting …
On the identification of differentially-active transcription factors ...
Oct 23, 2024 · Here we benchmark methods for differential TF activity inference from ATAC-seq. We curated a set of ATAC-seq datasets with replicates, profiling genome-wide accessibility …