dbCoRC: a database of core transcriptional regulatory circuitries modeled by H3K27ac ChIP-seq signals.
dbCoRC: a database of core transcriptional regulatory circuitries modeled by H3K27ac ChIP-seq signals.
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DOI：
10.1093/nar/gkx796
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发表时间：
2018-01-04
影响因子：
14.9
通讯作者：
Koeffler HP
中科院分区：
文献类型：
--
作者：
Huang M;Chen Y;Yang M;Guo A;Xu Y;Xu L;Koeffler HP
核心转录调控回路（CRC）是由一小群自我调节的转录因子（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已经揭示了CRCs在细胞身份和细胞命运的转录控制中的基本作用。需要系统地鉴定和随后存档不同细胞类型和组织中的CRC，以探索细胞/组织类型特异性和疾病相关的转录网络。在这里，我们提出了一个全面的和交互式的数据库（dbCoRC，http://dbcorc.cam-su.org）的CRC模型，这是计算推断从映射的超级增强子和TF结合位点的预测。当前版本的dbCoRC包含188个人和50个鼠细胞系/组织样本的CRC模型。与CRC模型一起，该数据库还提供：（i）单个样品的超级增强子、典型增强子和H3 K27 ac景观，（ii）CRC内每个核心TF跨超级增强子区域的推定结合位点和（iii）每个核心TF在正常或癌细胞/组织中的表达。dbCoRC将作为一个宝贵的资源，为科学界探索转录控制和调控电路的生物过程中，有关，但不限于谱系规范，组织稳态和肿瘤发生。
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.
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DOI：
10.1093/bioinformatics/btr064
发表时间：
2011-04-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Grant CE;Bailey TL;Noble WS
通讯作者：
Noble WS
影响因子：
64.5
作者：
Neph S;Stergachis AB;Reynolds A;Sandstrom R;Borenstein E;Stamatoyannopoulos JA
通讯作者：
Stamatoyannopoulos JA
在发育，重编程和肿瘤发生过程中，视网膜的动态表观遗传景观。
影响因子：
16.2
作者：
Aldiri I;Xu B;Wang L;Chen X;Hiler D;Griffiths L;Valentine M;Shirinifard A;Thiagarajan S;Sablauer A;Barabas ME;Zhang J;Johnson D;Frase S;Zhou X;Easton J;Zhang J;Mardis ER;Wilson RK;Downing JR;Dyer MA;St. Jude Children’s Research Hospital—Washington University Pediatric Cancer Genome Project
通讯作者：
St. Jude Children’s Research Hospital—Washington University Pediatric Cancer Genome Project
人肝细胞中的核心转录调节电路。
影响因子：
9.9
作者：
通讯作者：
--
影响因子：
64.5
作者：
Hnisz D;Abraham BJ;Lee TI;Lau A;Saint-André V;Sigova AA;Hoke HA;Young RA
通讯作者：
Young RA