• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利：CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2026

文献检索

告别复杂PubMed语法，用中文像聊天一样搜索，搜遍4000万医学文献。AI智能推荐，让科研检索更轻松。

立即免费搜索

文件翻译

保留排版，准确专业，支持PDF/Word/PPT等文件格式，支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述，25分钟生成高质量综述，智能提取关键信息，辅助科研写作。

立即免费体验

SuperTAD：利用优化的结构信息进行稳健的层次拓扑关联域检测。

SuperTAD: robust detection of hierarchical topologically associated domains with optimized structural information.

机构信息

Department of Computer Science, City University of Hong Kong, 83 Tat Chee Ave, Kowloon Tong, Hong Kong, China.

出版信息

Genome Biol. 2021 Jan 25;22(1):45. doi: 10.1186/s13059-020-02234-6.

DOI:10.1186/s13059-020-02234-6
PMID:33494803
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7831269/
Abstract

Topologically associating domains (TADs) are the organizational units of chromosome structures. TADs can contain TADs, thus forming a hierarchy. TAD hierarchies can be inferred from Hi-C data through coding trees. However, the current method for computing coding trees is not optimal. In this paper, we propose optimal algorithms for this computation. In comparison with seven state-of-art methods using two public datasets, from GM12878 and IMR90 cells, SuperTAD shows a significant enrichment of structural proteins around detected boundaries and histone modifications within TADs and displays a high consistency between various resolutions of identical Hi-C matrices.

摘要

拓扑关联域（TAD）是染色体结构的组织单元。TAD 可以包含 TAD，从而形成层次结构。TAD 层次结构可以通过编码树从 Hi-C 数据中推断出来。然而，当前计算编码树的方法不是最优的。在本文中，我们为此计算提出了最优算法。通过使用 GM12878 和 IMR90 细胞的两个公共数据集与七种最先进的方法进行比较，SuperTAD 在检测到的边界周围和 TAD 内的结构蛋白和组蛋白修饰方面表现出显著的富集，并且在相同 Hi-C 矩阵的各种分辨率之间显示出高度的一致性。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e9c9/7831269/33ed0f181590/13059_2020_2234_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e9c9/7831269/0dc9df023510/13059_2020_2234_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e9c9/7831269/d9495c0ecced/13059_2020_2234_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e9c9/7831269/b821bed6f7f8/13059_2020_2234_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e9c9/7831269/33ed0f181590/13059_2020_2234_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e9c9/7831269/0dc9df023510/13059_2020_2234_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e9c9/7831269/d9495c0ecced/13059_2020_2234_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e9c9/7831269/b821bed6f7f8/13059_2020_2234_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e9c9/7831269/33ed0f181590/13059_2020_2234_Fig4_HTML.jpg

相似文献

1
SuperTAD: robust detection of hierarchical topologically associated domains with optimized structural information.SuperTAD：利用优化的结构信息进行稳健的层次拓扑关联域检测。
Genome Biol. 2021 Jan 25;22(1):45. doi: 10.1186/s13059-020-02234-6.
2
SuperTAD-Fast: Accelerating Topologically Associating Domains Detection Through Discretization.SuperTAD-Fast：通过离散化加速拓扑关联结构域检测。
J Comput Biol. 2024 Sep;31(9):784-796. doi: 10.1089/cmb.2024.0490. Epub 2024 Jul 24.
3
SpectralTAD: an R package for defining a hierarchy of topologically associated domains using spectral clustering.SpectralTAD：一个使用谱聚类定义层次结构拓扑关联域的 R 包。
BMC Bioinformatics. 2020 Jul 20;21(1):319. doi: 10.1186/s12859-020-03652-w.
4
CATAD: exploring topologically associating domains from an insight of core-attachment structure.CATAD：从核心附着结构的角度探索拓扑关联结构域。
Brief Bioinform. 2023 Jul 20;24(4). doi: 10.1093/bib/bbad204.
5
TADKB: Family classification and a knowledge base of topologically associating domains.TADKB：拓扑关联域的家族分类和知识库。
BMC Genomics. 2019 Mar 14;20(1):217. doi: 10.1186/s12864-019-5551-2.
6
A computational method to predict topologically associating domain boundaries combining histone Marks and sequence information.一种结合组蛋白标记和序列信息预测拓扑关联结构域边界的计算方法。
BMC Genomics. 2019 Dec 27;20(Suppl 13):980. doi: 10.1186/s12864-019-6303-z.
7
A comparison of topologically associating domain callers over mammals at high resolution.在高分辨率下比较哺乳动物的拓扑关联结构域调用器。
BMC Bioinformatics. 2022 Apr 12;23(1):127. doi: 10.1186/s12859-022-04674-2.
8
Detecting TAD-like domains from RNA-associated interactions.从 RNA 相关相互作用中检测 TAD 样结构域。
Nucleic Acids Res. 2022 Aug 26;50(15):e88. doi: 10.1093/nar/gkac422.
9
A Comparison of Topologically Associating Domain Callers Based on Hi-C Data.基于 Hi-C 数据的拓扑关联域调用器比较。
IEEE/ACM Trans Comput Biol Bioinform. 2023 Jan-Feb;20(1):15-29. doi: 10.1109/TCBB.2022.3147805. Epub 2023 Feb 3.
10
LPAD: using network construction and label propagation to detect topologically associating domains from Hi-C data.LPAD：使用网络构建和标签传播从 Hi-C 数据中检测拓扑关联结构域。
Brief Bioinform. 2023 May 19;24(3). doi: 10.1093/bib/bbad165.

引用本文的文献

1
Topology entropy: Enhancing graph partitioning for TAD identification and single-cell clustering.拓扑熵：增强用于拓扑相关结构域识别和单细胞聚类的图划分
Comput Struct Biotechnol J. 2025 Apr 30;27:1864-1886. doi: 10.1016/j.csbj.2025.04.037. eCollection 2025.
2
RobusTAD: reference panel based annotation of nested topologically associating domains.RobusTAD：基于参考面板的嵌套拓扑相关结构域注释
Genome Biol. 2025 May 19;26(1):129. doi: 10.1186/s13059-025-03568-9.
3
deepTAD: an approach for identifying topologically associated domains based on convolutional neural network and transformer model.

本文引用的文献

1
OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries.OnTAD：层次结构域揭示了 TAD 和边界之间活性的分歧。
Genome Biol. 2019 Dec 18;20(1):282. doi: 10.1186/s13059-019-1893-y.
2
Technologies to study spatial genome organization: beyond 3C.研究空间基因组组织的技术：超越 3C。
Brief Funct Genomics. 2019 Nov 19;18(6):395-401. doi: 10.1093/bfgp/elz019.
3
Principles of genome folding into topologically associating domains.基因组折叠成拓扑关联域的原则。
深度TAD：一种基于卷积神经网络和Transformer模型识别拓扑相关结构域的方法。
Brief Bioinform. 2025 Mar 4;26(2). doi: 10.1093/bib/bbaf127.
4
Overcoming artificial structures in resolution-enhanced Hi-C data by signal decomposition and multi-scale attention.通过信号分解和多尺度注意力克服分辨率增强的Hi-C数据中的人工结构。
bioRxiv. 2024 Oct 24:2024.10.21.619560. doi: 10.1101/2024.10.21.619560.
5
A comprehensive benchmarking with interpretation and operational guidance for the hierarchy of topologically associating domains.针对拓扑关联结构域层次结构的综合基准测试、解释和操作指南。
Nat Commun. 2024 May 23;15(1):4376. doi: 10.1038/s41467-024-48593-7.
6
Identifying TAD-like domains on single-cell Hi-C data by graph embedding and changepoint detection.基于图嵌入和突变检测识别单细胞 Hi-C 数据中的 TAD 样结构域。
Bioinformatics. 2024 Mar 4;40(3). doi: 10.1093/bioinformatics/btae138.
7
Three-Dimensional Gene Regulation Network in Glioblastoma Ferroptosis.胶质母细胞瘤铁死亡的三维基因调控网络。
Int J Mol Sci. 2023 Oct 6;24(19):14945. doi: 10.3390/ijms241914945.
8
The shape of chromatin: insights from computational recognition of geometric patterns in Hi-C data.染色质的形态：Hi-C 数据中几何模式的计算识别带来的新见解。
Brief Bioinform. 2023 Sep 20;24(5). doi: 10.1093/bib/bbad302.
9
Mapping the semi-nested community structure of 3D chromosome contact networks.绘制三维染色体接触网络的半嵌套群落结构图谱。
PLoS Comput Biol. 2023 Jul 11;19(7):e1011185. doi: 10.1371/journal.pcbi.1011185. eCollection 2023 Jul.
10
DeDoc2 Identifies and Characterizes the Hierarchy and Dynamics of Chromatin TAD-Like Domains in the Single Cells.DeDoc2 鉴定并描述了单细胞染色质 TAD 样结构域的层次结构和动力学特征。
Adv Sci (Weinh). 2023 Jul;10(20):e2300366. doi: 10.1002/advs.202300366. Epub 2023 May 10.
Sci Adv. 2019 Apr 10;5(4):eaaw1668. doi: 10.1126/sciadv.aaw1668. eCollection 2019 Apr.
4
Comparison of computational methods for the identification of topologically associating domains.拓扑关联域识别的计算方法比较。
Genome Biol. 2018 Dec 10;19(1):217. doi: 10.1186/s13059-018-1596-9.
5
Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells.超分辨率染色质追踪揭示了单细胞中的域和协同相互作用。
Science. 2018 Oct 26;362(6413). doi: 10.1126/science.aau1783.
6
Decoding topologically associating domains with ultra-low resolution Hi-C data by graph structural entropy.通过图结构熵对超分辨 Hi-C 数据进行拓扑关联域解码。
Nat Commun. 2018 Aug 15;9(1):3265. doi: 10.1038/s41467-018-05691-7.
7
3C and 3C-based techniques: the powerful tools for spatial genome organization deciphering.3C及基于3C的技术：解析空间基因组组织的强大工具。
Mol Cytogenet. 2018 Mar 9;11:21. doi: 10.1186/s13039-018-0368-2. eCollection 2018.
8
High-resolution TADs reveal DNA sequences underlying genome organization in flies.高分辨率拓扑关联结构域揭示果蝇基因组组织背后的DNA序列。
Nat Commun. 2018 Jan 15;9(1):189. doi: 10.1038/s41467-017-02525-w.
9
Detecting hierarchical genome folding with network modularity.基于网络模块性探测层级基因组折叠。
Nat Methods. 2018 Feb;15(2):119-122. doi: 10.1038/nmeth.4560. Epub 2018 Jan 15.
10
Identifying topologically associating domains and subdomains by Gaussian Mixture model And Proportion test.通过高斯混合模型和比例检验识别拓扑相关结构域和亚结构域。
Nat Commun. 2017 Sep 14;8(1):535. doi: 10.1038/s41467-017-00478-8.