PT  - JOURNAL ARTICLE
AU  - Shengquan Chen
AU  - Yong Wang
AU  - Rui Jiang
TI  - OPENANNO: annotating genomic regions with chromatin accessibility
AID  - 10.1101/596627
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 596627
4099  - http://biorxiv.org/content/early/2020/07/14/596627.short
4100  - http://biorxiv.org/content/early/2020/07/14/596627.full
AB  - Chromatin accessibility, as a powerful marker of active DNA regulatory elements, provides rich information to understand the regulatory mechanism. The revolution in high-throughput methods has accumulated massive chromatin accessibility profiles in public repositories as a valuable resource for machine learning and integrative studies. Nevertheless, utilization of these data is often hampered by the cumbersome and time-consuming collection, processing, and annotation of the chromatin accessibility information. Motivated by the above understanding, we developed a web server, named OPENANNO, to annotate the openness of genomic regions across diverse cell lines, tissues, and systems. The annotation is based on 871 DNase-seq experiments across 199 cell lines, 48 tissues, and 11 systems from ENCODE, and openness values rigorously defined by four statistical strategies. Particularly, we designed a parallel program to allow efficient annotation and visualization of the openness of a vast amount of genomic regions. OPENANNO will help users extract and download formulated data in a batch follow-up analysis. Besides, we illustrate the valuable information provided by OPENANNO using an enhancer of blood vessels from VISTA Enhancer Browser as an example. Furthermore, we demonstrate three applications of OPENANNO in regulatory mechanism and association studies. We believe that OPENANNO will serve as a comprehensive and user-friendly web server to facilitate methodology development and biological insights discovery, specifically to explore the biological questions and model the regulatory landscape of genome. OPENANNO is freely available at http://bioinfo.au.tsinghua.edu.cn/openness/anno/ or http://166.111.5.208:65424/openness/anno/.Competing Interest StatementThe authors have declared no competing interest.