Tool:SPACE: a web tool for exploring chromatin accessibility in cancers based on ATAC-seq

Question

[wuyc]

A hallmark of cancer is the abnormal chromatin accessibility. The Cancer Genome Atlas has documented a wealth of ATAC-seq data which detect the DNA accessibility (Corces et al., Science 2018). However, a user-friendly tool for cancer biologists to conveniently explore and visualize ATAC-seq data is still lacking. Here, we developed an interactive web application, Shiny Pan-cancer Accessible Chromatin Explorer (SPACE), as a public resource to analyze the chromatin accessibility in a comprehensive and flexible manner.

In SPACE, users can:

• 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 peaks;
• Explore the role of peaks in the tumor immune microenvironment;
• Investigate correlations between TFs/mRNAs/lncRNAs/miRNAs and peaks across cancers;

keywords: atac-seq, database, cancer, chromatin accessibility.

SPACE is available at http://fun-science.club/SPACE/

[wuyc]

SPACE is available at http://fun-science.club/SPACE/