dbCoRC:一个基于 H3K27ac ChIP-seq 信号建模的核心转录调控回路数据库。
dbCoRC: a database of core transcriptional regulatory circuitries modeled by H3K27ac ChIP-seq signals.
机构信息
School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China.
Cancer Science Institute of Singapore, National University of Singapore 117599, Singapore.
出版信息
Nucleic Acids Res. 2018 Jan 4;46(D1):D71-D77. doi: 10.1093/nar/gkx796.
Core transcription regulatory circuitry (CRC) is comprised of a small group of self-regulated transcription factors (TFs) and their interconnected regulatory loops. Studies from embryonic stem cells and other cellular models have revealed the elementary roles of CRCs in transcriptional control of cell identity and cellular fate. Systematic identification and subsequent archiving of CRCs across diverse cell types and tissues are needed to explore both cell/tissue type-specific and disease-associated transcriptional networks. Here, we present a comprehensive and interactive database (dbCoRC, http://dbcorc.cam-su.org) of CRC models which are computationally inferred from mapping of super-enhancer and prediction of TF binding sites. The current version of dbCoRC contains CRC models for 188 human and 50 murine cell lines/tissue samples. In companion with CRC models, this database also provides: (i) super enhancer, typical enhancer, and H3K27ac landscape for individual samples, (ii) putative binding sites of each core TF across the super-enhancer regions within CRC and (iii) expression of each core TF in normal or cancer cells/tissues. The dbCoRC will serve as a valuable resource for the scientific community to explore transcriptional control and regulatory circuitries in biological processes related to, but not limited to lineage specification, tissue homeostasis and tumorigenesis.
核心转录调控回路 (CRC) 由一小群自我调控的转录因子 (TF) 及其相互连接的调控环组成。来自胚胎干细胞和其他细胞模型的研究揭示了 CRC 在细胞身份和细胞命运的转录控制中的基本作用。需要对不同细胞类型和组织中的 CRC 进行系统的识别和随后的存档,以探索细胞/组织类型特异性和与疾病相关的转录网络。在这里,我们展示了一个全面和交互式的数据库 (dbCoRC,http://dbcorc.cam-su.org),其中包含通过超级增强子映射和 TF 结合位点预测计算推断出的 CRC 模型。当前版本的 dbCoRC 包含 188 个人类和 50 个鼠类细胞系/组织样本的 CRC 模型。与 CRC 模型一起,该数据库还提供了:(i) 单个样本的超级增强子、典型增强子和 H3K27ac 景观,(ii) CRC 内超级增强子区域中每个核心 TF 的假定结合位点,以及 (iii) 正常或癌细胞/组织中每个核心 TF 的表达。dbCoRC 将成为科学界的宝贵资源,用于探索与谱系特化、组织稳态和肿瘤发生等相关但不限于这些过程的转录控制和调控回路。