• 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

AnnoMiner 是一种新的网络工具，用于整合表观遗传学、转录因子占据和转录组学数据，以预测转录调控因子。

AnnoMiner is a new web-tool to integrate epigenetics, transcription factor occupancy and transcriptomics data to predict transcriptional regulators.

机构信息

Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.

Aix-Marseille University, CNRS, IBDM UMR 7288, The Turing Centre for Living systems (CENTURI), Aix-Marseille University, Parc Scientifique de Luminy Case 907, 163, Avenue de Luminy, 13009, Marseille, France.

出版信息

Sci Rep. 2021 Jul 29;11(1):15463. doi: 10.1038/s41598-021-94805-1.

DOI:10.1038/s41598-021-94805-1
PMID:34326396
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8322331/
Abstract

Gene expression regulation requires precise transcriptional programs, led by transcription factors in combination with epigenetic events. Recent advances in epigenomic and transcriptomic techniques provided insight into different gene regulation mechanisms. However, to date it remains challenging to understand how combinations of transcription factors together with epigenetic events control cell-type specific gene expression. We have developed the AnnoMiner web-server, an innovative and flexible tool to annotate and integrate epigenetic, and transcription factor occupancy data. First, AnnoMiner annotates user-provided peaks with gene features. Second, AnnoMiner can integrate genome binding data from two different transcriptional regulators together with gene features. Third, AnnoMiner offers to explore the transcriptional deregulation of genes nearby, or within a specified genomic region surrounding a user-provided peak. AnnoMiner's fourth function performs transcription factor or histone modification enrichment analysis for user-provided gene lists by utilizing hundreds of public, high-quality datasets from ENCODE for the model organisms human, mouse, Drosophila and C. elegans. Thus, AnnoMiner can predict transcriptional regulators for a studied process without the strict need for chromatin data from the same process. We compared AnnoMiner to existing tools and experimentally validated several transcriptional regulators predicted by AnnoMiner to indeed contribute to muscle morphogenesis in Drosophila. AnnoMiner is freely available at http://chimborazo.ibdm.univ-mrs.fr/AnnoMiner/ .

摘要

基因表达调控需要精确的转录程序，由转录因子与表观遗传事件共同主导。近年来，表观基因组学和转录组学技术的进步为理解不同的基因调控机制提供了线索。然而，迄今为止，理解转录因子与表观遗传事件如何共同控制细胞类型特异性基因表达仍然具有挑战性。我们开发了 AnnoMiner 网络服务器，这是一种创新且灵活的工具，用于注释和整合表观遗传和转录因子占据数据。首先，AnnoMiner 用基因特征注释用户提供的峰。其次，AnnoMiner 可以整合来自两个不同转录调节剂的基因组结合数据以及基因特征。第三，AnnoMiner 提供了一种方法来探索附近基因或用户提供的峰周围指定基因组区域内基因的转录失调。AnnoMiner 的第四个功能是通过利用来自人类、小鼠、果蝇和秀丽隐杆线虫等模式生物的数百个高质量 ENCODE 公共数据集，对用户提供的基因列表进行转录因子或组蛋白修饰富集分析。因此，AnnoMiner 可以预测研究过程中的转录调节剂，而无需严格要求来自同一过程的染色质数据。我们将 AnnoMiner 与现有工具进行了比较，并通过实验验证了 AnnoMiner 预测的几个转录调节剂确实有助于果蝇的肌肉形态发生。AnnoMiner 可免费在 http://chimborazo.ibdm.univ-mrs.fr/AnnoMiner/ 获得。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3421/8322331/e4d0059daa7e/41598_2021_94805_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3421/8322331/673dbcad069c/41598_2021_94805_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3421/8322331/170123bbd699/41598_2021_94805_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3421/8322331/2512a73ce688/41598_2021_94805_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3421/8322331/f3d4e3b1ffe7/41598_2021_94805_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3421/8322331/ea0b321f0923/41598_2021_94805_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3421/8322331/a6896fbb3d1e/41598_2021_94805_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3421/8322331/bb2d6028955d/41598_2021_94805_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3421/8322331/e4d0059daa7e/41598_2021_94805_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3421/8322331/673dbcad069c/41598_2021_94805_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3421/8322331/170123bbd699/41598_2021_94805_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3421/8322331/2512a73ce688/41598_2021_94805_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3421/8322331/f3d4e3b1ffe7/41598_2021_94805_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3421/8322331/ea0b321f0923/41598_2021_94805_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3421/8322331/a6896fbb3d1e/41598_2021_94805_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3421/8322331/bb2d6028955d/41598_2021_94805_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3421/8322331/e4d0059daa7e/41598_2021_94805_Fig8_HTML.jpg

相似文献

1
AnnoMiner is a new web-tool to integrate epigenetics, transcription factor occupancy and transcriptomics data to predict transcriptional regulators.AnnoMiner 是一种新的网络工具，用于整合表观遗传学、转录因子占据和转录组学数据，以预测转录调控因子。
Sci Rep. 2021 Jul 29;11(1):15463. doi: 10.1038/s41598-021-94805-1.
2
Transcriptomics and epigenetic data integration learning module on Google Cloud.转录组学和表观遗传学数据集成学习模块在谷歌云上。
Brief Bioinform. 2024 Jul 23;25(Supplement_1). doi: 10.1093/bib/bbae352.
3
Dynamic Regulatory Event Mining by iDREM in Large-Scale Multi-omics Datasets During Biotic and Abiotic Stress in Plants.植物在生物和非生物胁迫下通过 iDREM 在大规模多组学数据中进行动态调控事件挖掘。
Methods Mol Biol. 2021;2328:191-202. doi: 10.1007/978-1-0716-1534-8_12.
4
Gene set control analysis predicts hematopoietic control mechanisms from genome-wide transcription factor binding data.基因集调控分析预测了从全基因组转录因子结合数据中造血的调控机制。
Exp Hematol. 2013 Apr;41(4):354-66.e14. doi: 10.1016/j.exphem.2012.11.008. Epub 2012 Dec 4.
5
Development and application of an integrated allele-specific pipeline for methylomic and epigenomic analysis (MEA).开发和应用甲基化组学和表观基因组学分析（MEA）的综合等位基因特异性管道。
BMC Genomics. 2018 Jun 15;19(1):463. doi: 10.1186/s12864-018-4835-2.
6
Seqinspector: position-based navigation through the ChIP-seq data landscape to identify gene expression regulators.Seqinspector：通过ChIP-seq数据全景进行基于位置的导航，以识别基因表达调节因子。
BMC Bioinformatics. 2016 Feb 12;17:85. doi: 10.1186/s12859-016-0938-4.
7
i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly.i-cisTarget 2015更新：人类、小鼠和果蝇中的广义顺式调控富集分析
Nucleic Acids Res. 2015 Jul 1;43(W1):W57-64. doi: 10.1093/nar/gkv395. Epub 2015 Apr 29.
8
NUCLIZE for quantifying epigenome: generating histone modification data at single-nucleosome resolution using genuine nucleosome positions.NUCLIZE 用于定量表观基因组学：使用真实核小体位置在单个核小体分辨率下生成组蛋白修饰数据。
BMC Genomics. 2019 Jul 2;20(1):541. doi: 10.1186/s12864-019-5932-6.
9
Role of ChIP-seq in the discovery of transcription factor binding sites, differential gene regulation mechanism, epigenetic marks and beyond.染色质免疫沉淀测序（ChIP-seq）在转录因子结合位点发现、差异基因调控机制、表观遗传标记及其他方面的作用。
Cell Cycle. 2014;13(18):2847-52. doi: 10.4161/15384101.2014.949201.
10
The histone demethylase KDM3A regulates the transcriptional program of the androgen receptor in prostate cancer cells.组蛋白去甲基化酶KDM3A调节前列腺癌细胞中雄激素受体的转录程序。
Oncotarget. 2017 May 2;8(18):30328-30343. doi: 10.18632/oncotarget.15681.

引用本文的文献

1
Developmental remodelling of flight muscle sarcomeres: a scaled myofilament lattice model based on multiscale morphometrics.飞行肌肌节的发育重塑：基于多尺度形态计量学的缩放肌丝晶格模型。
Open Biol. 2025 Aug;15(8):250182. doi: 10.1098/rsob.250182. Epub 2025 Aug 13.
2
Simultaneous cellular and molecular phenotyping of embryonic mutants using single-cell regulatory trajectories.利用单细胞调控轨迹对胚胎突变体进行细胞和分子表型的同时分析。
Dev Cell. 2022 Feb 28;57(4):496-511.e8. doi: 10.1016/j.devcel.2022.01.016. Epub 2022 Feb 16.
3
Prednisolone rescues Duchenne muscular dystrophy phenotypes in human pluripotent stem cell-derived skeletal muscle in vitro.

本文引用的文献

1
GAF is essential for zygotic genome activation and chromatin accessibility in the early embryo.GAF 对于合子基因组激活和早期胚胎中的染色质可及性至关重要。
Elife. 2021 Mar 15;10:e66668. doi: 10.7554/eLife.66668.
2
The Hippo pathway controls myofibril assembly and muscle fiber growth by regulating sarcomeric gene expression.Hippo 通路通过调节肌节基因表达控制肌原纤维组装和肌肉纤维生长。
Elife. 2021 Jan 6;10:e63726. doi: 10.7554/eLife.63726.
3
Perspectives on ENCODE.ENCODE 之见。
泼尼松龙可挽救人多能干细胞体外分化骨骼肌中的杜氏肌营养不良表型。
Proc Natl Acad Sci U S A. 2021 Jul 13;118(28). doi: 10.1073/pnas.2022960118.
Nature. 2020 Jul;583(7818):693-698. doi: 10.1038/s41586-020-2449-8. Epub 2020 Jul 29.
4
Functional effects of variation in transcription factor binding highlight long-range gene regulation by epromoters.转录因子结合变异的功能效应突出了epromoters 对长程基因调控的作用。
Nucleic Acids Res. 2020 Apr 6;48(6):2866-2879. doi: 10.1093/nar/gkaa123.
5
The ENCODE Portal as an Epigenomics Resource.作为表观基因组学资源的ENCODE门户。
Curr Protoc Bioinformatics. 2019 Dec;68(1):e89. doi: 10.1002/cpbi.89.
6
TFEA.ChIP: a tool kit for transcription factor binding site enrichment analysis capitalizing on ChIP-seq datasets.TFEA.ChIP：一个转录因子结合位点富集分析工具包，利用 ChIP-seq 数据集。
Bioinformatics. 2019 Dec 15;35(24):5339-5340. doi: 10.1093/bioinformatics/btz573.
7
Benchmark and integration of resources for the estimation of human transcription factor activities.用于估计人类转录因子活性的资源的基准测试和整合。
Genome Res. 2019 Aug;29(8):1363-1375. doi: 10.1101/gr.240663.118. Epub 2019 Jul 24.
8
ChEA3: transcription factor enrichment analysis by orthogonal omics integration.ChEA3：通过正交组学整合进行转录因子富集分析。
Nucleic Acids Res. 2019 Jul 2;47(W1):W212-W224. doi: 10.1093/nar/gkz446.
9
Long-range enhancer-promoter contacts in gene expression control.长程增强子-启动子相互作用在基因表达调控中的作用。
Nat Rev Genet. 2019 Aug;20(8):437-455. doi: 10.1038/s41576-019-0128-0.
10
modEnrichr: a suite of gene set enrichment analysis tools for model organisms.modEnrichr：一套适用于模式生物的基因集富集分析工具。
Nucleic Acids Res. 2019 Jul 2;47(W1):W183-W190. doi: 10.1093/nar/gkz347.