SPACE: Shiny Pan-cancer Accessible Chromatin Explorer

Here, we develop Shiny Pan-cancer Accessible Chromatin Explorer (SPACE) as an all-in-one web server of 562,709 regulatory elements in 404 patients across 23 cancer types. SPACE is a database supporting ATAC-seq analysis with matched clinical phenotype and transcriptome data.

Link

http://fun-science.club/SPACE

SPACE supports

• Explore active DNA regulatory elements of genes;
• Search the potential binding TFs of peaks;
• View peak expression according to the clinical phenotypes such as cancer subtypes or patient prognosis;
• Compute the associated signalling pathways of regulatory elements;
• Explore the role of peaks in the tumor immune microenvironment;
• Investigate correlations between TFs/mRNAs/lncRNAs/miRNAs and peaks across cancers.

Methods

Available on SPACE website.

Data sourse

The Cancer Genome Atlas (Corces et al., Science 2018).

Contact

PI: Yihui Fan (fanyihui at ntu.edu.cn).
Technical problems: Yingcheng Wu (wuyc at usa.com).

Citations

• Yingcheng Wu, et al. SPACE: A web server for linking chromatin accessibility with clinical phenotypes and immune-microenvironment in pan-cancer. Cell Mol Immunol (2020).
• Corces MR, et al. The chromatin accessibility landscape of primary human cancers. Science (2018).