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预测患者特异性增强子-启动子相互作用。

Predicting patient-specific enhancer-promoter interactions.

机构信息

Wisconsin Institute for Discovery, 330 N. Orchard Street, Madison, WI 53715, USA; The Max Harry Weil Institute of Critical Care Research & Innovation, University of Michigan, Ann Arbor, MI, USA; Department of Emergency Medicine, University of Michigan Medical School, Ann Arbor, MI, USA.

Wisconsin Institute for Discovery, 330 N. Orchard Street, Madison, WI 53715, USA; Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53715, USA.

出版信息

Cell Rep Methods. 2023 Sep 25;3(9):100594. doi: 10.1016/j.crmeth.2023.100594.

DOI:10.1016/j.crmeth.2023.100594
PMID:37751694
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10545932/
Abstract

Computational methods that can predict hard-to-measure modalities from those that are easier to measure, in a patient-specific manner, play a critical role in personalized medicine. In this issue of Cell Reports Methods, Khurana et al. present differential gene targets of accessible chromatin (DGTAC), an approach which predicts patient-specific enhancer-promoter interactions.

摘要

能够以患者特异性方式从较易测量的模式预测难以测量的模式的计算方法在个性化医疗中起着关键作用。在本期《Cell Reports Methods》中,Khurana 等人提出了可及染色质的差异基因靶点(DGTAC)方法,该方法可预测患者特异性增强子-启动子相互作用。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/af9b/10545932/3f087452ddc5/gr1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/af9b/10545932/3f087452ddc5/gr1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/af9b/10545932/3f087452ddc5/gr1.jpg

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1
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2
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本文引用的文献

1
Recapitulation of patient-specific 3D chromatin conformation using machine learning.使用机器学习对患者特异性的 3D 染色质构象进行重构。
Cell Rep Methods. 2023 Sep 25;3(9):100578. doi: 10.1016/j.crmeth.2023.100578. Epub 2023 Sep 5.
2
Epiphany: predicting Hi-C contact maps from 1D epigenomic signals.顿悟:从一维表观基因组信号预测 Hi-C 接触图谱。
Genome Biol. 2023 Jun 6;24(1):134. doi: 10.1186/s13059-023-02934-9.
3
Multi-Omics Profiling for Health.多组学分析与健康。
Mol Cell Proteomics. 2023 Jun;22(6):100561. doi: 10.1016/j.mcpro.2023.100561. Epub 2023 Apr 27.
4
Cell-type-specific prediction of 3D chromatin organization enables high-throughput in silico genetic screening.细胞类型特异性预测 3D 染色质组织可实现高通量计算遗传筛选。
Nat Biotechnol. 2023 Aug;41(8):1140-1150. doi: 10.1038/s41587-022-01612-8. Epub 2023 Jan 9.
5
Transcriptional dysregulation by aberrant enhancer activation and rewiring in cancer.癌症中异常增强子激活和重布线导致的转录失调。
Cancer Sci. 2021 Jun;112(6):2081-2088. doi: 10.1111/cas.14884. Epub 2021 May 1.
6
DeepHiC: A generative adversarial network for enhancing Hi-C data resolution.DeepHiC:一种用于提高 Hi-C 数据分辨率的生成对抗网络。
PLoS Comput Biol. 2020 Feb 21;16(2):e1007287. doi: 10.1371/journal.pcbi.1007287. eCollection 2020 Feb.
7
Methods for mapping 3D chromosome architecture.3D 染色体构象的绘图方法。
Nat Rev Genet. 2020 Apr;21(4):207-226. doi: 10.1038/s41576-019-0195-2. Epub 2019 Dec 17.
8
In silico prediction of high-resolution Hi-C interaction matrices.基于计算机的高分辨率 Hi-C 互作矩阵预测。
Nat Commun. 2019 Dec 6;10(1):5449. doi: 10.1038/s41467-019-13423-8.
9
Computational Biology Solutions to Identify Enhancers-target Gene Pairs.用于识别增强子-靶基因对的计算生物学解决方案
Comput Struct Biotechnol J. 2019 Jun 14;17:821-831. doi: 10.1016/j.csbj.2019.06.012. eCollection 2019.
10
Reconstruction of enhancer-target networks in 935 samples of human primary cells, tissues and cell lines.在 935 个人类原代细胞、组织和细胞系样本中重建增强子-靶标网络。
Nat Genet. 2017 Oct;49(10):1428-1436. doi: 10.1038/ng.3950. Epub 2017 Sep 4.