Cistrome Explorer：用于大规模表观基因组数据的交互式可视化分析工具。
Cistrome Explorer: an interactive visual analysis tool for large-scale epigenomic data.
机构信息
Department of Biomedical Informatics, Harvard Medical School.
Department of Data Science, Harvard T.H. Chan School of Public Health, Dana-Farber Cancer Institute.
出版信息
Bioinformatics. 2023 Feb 3;39(2). doi: 10.1093/bioinformatics/btad018.
SUMMARY
The regulation of genes by cis-regulatory elements (CREs) is complex and differs between cell types. Visual analysis of large collections of chromatin profiles across diverse cell types, integrated with computational methods, can reveal meaningful biological insights. We developed Cistrome Explorer, a web-based interactive visual analytics tool for exploring thousands of chromatin profiles in diverse cell types. Integrated with the Cistrome Data Browser database which contains thousands of ChIP-seq, DNase-seq and ATAC-seq samples, Cistrome Explorer enables the discovery of patterns of CREs across cell types and the identification of transcription factor binding underlying these patterns.
AVAILABILITY AND IMPLEMENTATION
Cistrome Explorer and its source code are available at http://cisvis.gehlenborglab.org/ and released under the MIT License. Documentation can be accessed via http://cisvis.gehlenborglab.org/docs/.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
顺式调控元件 (CRE) 对基因的调控非常复杂，并且在不同细胞类型之间存在差异。通过对不同细胞类型的大量染色质谱进行计算方法与可视化分析的整合，可以揭示有意义的生物学见解。我们开发了 Cistrome Explorer，这是一种基于网络的交互式可视化分析工具，可用于探索多种细胞类型中的数千个染色质谱。它与包含数千个 ChIP-seq、DNase-seq 和 ATAC-seq 样本的 Cistrome Data Browser 数据库集成，Cistrome Explorer 能够发现细胞类型之间 CRE 模式，并识别这些模式下的转录因子结合。
可用性和实现
Cistrome Explorer 及其源代码可在 http://cisvis.gehlenborglab.org/ 上获得，并根据 MIT 许可证发布。文档可通过 http://cisvis.gehlenborglab.org/docs/ 访问。
补充信息
补充数据可在《生物信息学》在线获得。
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