GNNMF-ATAC: A Web Server-Based ATAC-seq Motif Finding and Annotation Analysis

Transcription Factor Binding Sites (TFBSs) are specific DNA sequences that promote or inhibit gene expression via binding regions, thereby affecting protein synthesis. TFBSs play a crucial role in gene regulatory networks, complex diseases, and the growth of humans. Assay for Transposase-Accessible Chromatin with high-throughput Sequencing (ATAC-seq) is a high-throughput sequencing technology, providing a new perspective for studying transcription factor binding patterns (motifs). Different from sequencing ChIP-seq technologies, ATAC-seq is more efficient in detecting binding sites. Methods based on graph neural network have success on ATAC-seq motifs, but researchers make considerable effort to deploy these models. To address this issue, we developed a web server named GNNMF-ATAC for users. GNNMF-ATAC provides TFBSs prediction, motif finding, and enrichment analysis via deploying tools. Moreover, GNNMF-ATAC provides motif finding results and visualizations of 200 humans and 80 mouse ENCODE ATAC-seq datasets. GNNMF-ATAC is a valuable resource for experimental biologists seeking a user-friendly tool to find ATAC-seq motifs without programming expertise. GNNMF-ATAC is freely available at http://gnnmf.online.