Welcome to OpenAnnotate, a web server for efficiently annotating the chromatin accessibility of genomic regions
Chromatin accessibility is a measure of the ability of nuclear macromolecules to physically contact DNA, and is essential for understanding regulatory mechanisms.
OpenAnnotate facilitates the chromatin accessibility annotation for massive genomic regions by allowing ultra-efficient annotation across various biosample types based on chromatin accessibility profiles accumulated in public repositories (1236 samples from ENCODE and 1493 samples from ATACdb).
OpenAnnotate has been successfully applied to studies of regulatory mechanism, and sheds light on single-cell data analyses.
- Illustrate the usage of OpenAnnotate
- Analyse cell type-specificity of enhancers
- OpenAnnotate has been applied in Nucleic Acids Research 2021 and Proceedings of the National Academy of Sciences 2020.
- Walk through a deep learning model
- Compare to the model without openness
- OpenAnnotate has been applied in Nucleic Acids Research 2019 and Genomics, Proteomics & Bioinformatics 2021.
- Introduce a reference-based approach
- Evaluate by visualization and clustering
- The reference-based idea has been applied in Cell 2018, Nature Communications 2021 and Genome Biology 2020.