CATA: a comprehensive chromatin accessibility database for cancer. (17th January 2022)

• Record Type: Journal Article
• Authors: Zhou, Jianyuan; Li, Yanshang; Cao, Haotian; Yang, Min; Chu, Lingyu; Li, Taisong; Yu, Zhengmin; Yu, Rui; Qiu, Bo; Wang, Qiuyu; Li, Xuecang; Xie, Jianjun
• Is Part Of: Database. Volume 2022(2022)
• Publication Date: 2022-01-17
• Subjects: Biology -- Databases -- Periodicals; Bioinformatics -- Periodicals; 570.285
• DOI: 10.1093/database/baab085
• Languages: English
• ISSNs: 1758-0463

Abstract

Abstract: Accessible chromatin refers to the active regions of a chromosome that are bound by many transcription factors (TFs). Changes in chromatin accessibility play a critical role in tumorigenesis. With the emergence of novel methods like Assay for Transposase-accessible Chromatin Sequencing, a sequencing method that maps chromatin-accessible regions (CARs) and enables the computational analysis of TF binding at chromatin-accessible sites, the regulatory landscape in cancer can be dissected. Herein, we developed a comprehensive cancer chromatin accessibility database named CATA, which aims to provide available resources of cancer CARs and to annotate their potential roles in the regulation of genes in a cancer type-specific manner. In this version, CATA stores 2 991 163 CARs from 23 cancer types, binding information of 1398 TFs within the CARs, and provides multiple annotations about these regions, including common single nucleotide polymorphisms (SNPs), risk SNPs, copy number variation, somatic mutations, motif changes, expression quantitative trait loci, methylation and CRISPR/Cas9 target loci. Moreover, CATA supports cancer survival analysis of the CAR-associated genes and provides detailed clinical information of the tumor samples. Database URL : CATA is available at http://www.xiejjlab.bio/cata/ .