• 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

拟南芥类异戊二烯基因网络的稀疏图形高斯建模

Sparse graphical Gaussian modeling of the isoprenoid gene network in Arabidopsis thaliana.

作者信息

Wille Anja, Zimmermann Philip, Vranová Eva, Fürholz Andreas, Laule Oliver, Bleuler Stefan, Hennig Lars, Prelic Amela, von Rohr Peter, Thiele Lothar, Zitzler Eckart, Gruissem Wilhelm, Bühlmann Peter

机构信息

Reverse Engineering Group, Swiss Federal Institute of Technology (ETH), Zurich.

出版信息

Genome Biol. 2004;5(11):R92. doi: 10.1186/gb-2004-5-11-r92. Epub 2004 Oct 25.

DOI:10.1186/gb-2004-5-11-r92
PMID:15535868
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC545783/
Abstract

We present a novel graphical Gaussian modeling approach for reverse engineering of genetic regulatory networks with many genes and few observations. When applying our approach to infer a gene network for isoprenoid biosynthesis in Arabidopsis thaliana, we detect modules of closely connected genes and candidate genes for possible cross-talk between the isoprenoid pathways. Genes of downstream pathways also fit well into the network. We evaluate our approach in a simulation study and using the yeast galactose network.

摘要

我们提出了一种新颖的图形高斯建模方法，用于对具有多个基因和少量观测值的遗传调控网络进行逆向工程。当将我们的方法应用于推断拟南芥中类异戊二烯生物合成的基因网络时，我们检测到紧密连接的基因模块以及类异戊二烯途径之间可能存在串扰的候选基因。下游途径的基因也很好地融入了该网络。我们在模拟研究中并使用酵母半乳糖网络对我们的方法进行了评估。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7f72/545783/ec4988b49afc/gb-2004-5-11-r92-6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7f72/545783/4358ec9dc1d3/gb-2004-5-11-r92-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7f72/545783/1c65b351d7a5/gb-2004-5-11-r92-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7f72/545783/0d927c18efda/gb-2004-5-11-r92-3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7f72/545783/91a0290718cd/gb-2004-5-11-r92-4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7f72/545783/0640484fef22/gb-2004-5-11-r92-5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7f72/545783/ec4988b49afc/gb-2004-5-11-r92-6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7f72/545783/4358ec9dc1d3/gb-2004-5-11-r92-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7f72/545783/1c65b351d7a5/gb-2004-5-11-r92-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7f72/545783/0d927c18efda/gb-2004-5-11-r92-3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7f72/545783/91a0290718cd/gb-2004-5-11-r92-4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7f72/545783/0640484fef22/gb-2004-5-11-r92-5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7f72/545783/ec4988b49afc/gb-2004-5-11-r92-6.jpg

相似文献

1
Sparse graphical Gaussian modeling of the isoprenoid gene network in Arabidopsis thaliana.拟南芥类异戊二烯基因网络的稀疏图形高斯建模
Genome Biol. 2004;5(11):R92. doi: 10.1186/gb-2004-5-11-r92. Epub 2004 Oct 25.
2
Learning an L1-regularized Gaussian Bayesian network in the equivalence class space.在等价类空间中学习L1正则化高斯贝叶斯网络。
IEEE Trans Syst Man Cybern B Cybern. 2010 Oct;40(5):1231-42. doi: 10.1109/TSMCB.2009.2036593. Epub 2010 Jan 15.
3
Gradient directed regularization for sparse Gaussian concentration graphs, with applications to inference of genetic networks.用于稀疏高斯浓度图的梯度导向正则化及其在遗传网络推断中的应用
Biostatistics. 2006 Apr;7(2):302-17. doi: 10.1093/biostatistics/kxj008. Epub 2005 Dec 2.
4
A comparative study of covariance selection models for the inference of gene regulatory networks.协方差选择模型在基因调控网络推断中的比较研究。
J Biomed Inform. 2013 Oct;46(5):894-904. doi: 10.1016/j.jbi.2013.07.002. Epub 2013 Jul 20.
5
Quantitative inference of dynamic regulatory pathways via microarray data.通过微阵列数据对动态调控途径进行定量推断。
BMC Bioinformatics. 2005 Mar 7;6:44. doi: 10.1186/1471-2105-6-44.
6
Weighted lasso in graphical Gaussian modeling for large gene network estimation based on microarray data.基于微阵列数据的大型基因网络估计的图形高斯建模中的加权套索法
Genome Inform. 2007;19:142-53.
7
AGRIS: Arabidopsis gene regulatory information server, an information resource of Arabidopsis cis-regulatory elements and transcription factors.AGRIS：拟南芥基因调控信息服务器，一个关于拟南芥顺式调控元件和转录因子的信息资源。
BMC Bioinformatics. 2003 Jun 23;4:25. doi: 10.1186/1471-2105-4-25.
8
AtIPD: a curated database of Arabidopsis isoprenoid pathway models and genes for isoprenoid network analysis.AtIPD：一个经过整理的拟南芥类异戊二烯途径模型和用于类异戊二烯网络分析的基因数据库。
Plant Physiol. 2011 Aug;156(4):1655-60. doi: 10.1104/pp.111.177758. Epub 2011 May 26.
9
Comprehensive Assessment of Transcriptional Regulation Facilitates Metabolic Engineering of Isoprenoid Accumulation in Arabidopsis.转录调控的综合评估有助于拟南芥中类异戊二烯积累的代谢工程。
Plant Physiol. 2015 Nov;169(3):1595-606. doi: 10.1104/pp.15.00573. Epub 2015 Aug 17.
10
Dynamics of the genetic regulatory network for Arabidopsis thaliana flower morphogenesis.拟南芥花形态发生的基因调控网络动态
J Theor Biol. 1998 Jul 27;193(2):307-19. doi: 10.1006/jtbi.1998.0701.

引用本文的文献

1
SingleCellGGM enables gene expression program identification from single-cell transcriptomes and facilitates universal cell label transfer.SingleCellGGM 能够从单细胞转录组中识别基因表达程序，并促进通用细胞标签转移。
Cell Rep Methods. 2024 Jul 15;4(7):100813. doi: 10.1016/j.crmeth.2024.100813. Epub 2024 Jul 5.
2
Single-cell network analysis reveals gene expression programs for Arabidopsis root development and metabolism.单细胞网络分析揭示了拟南芥根系发育和代谢的基因表达程序。
Plant Commun. 2024 Aug 12;5(8):100978. doi: 10.1016/j.xplc.2024.100978. Epub 2024 May 22.
3
Methyl-Jasmonate Functions as a Molecular Switch Promoting Cross-Talk between Pathways for the Biosynthesis of Isoprenoid Backbones Used to Modify Proteins in Plants.

本文引用的文献

1
Integrating high-throughput and computational data elucidates bacterial networks.整合高通量和计算数据可阐明细菌网络。
Nature. 2004 May 6;429(6987):92-6. doi: 10.1038/nature02456.
2
Development and evaluation of an Arabidopsis whole genome Affymetrix probe array.拟南芥全基因组Affymetrix探针阵列的开发与评估。
Plant J. 2004 May;38(3):545-61. doi: 10.1111/j.1365-313X.2004.02061.x.
3
The Arabidopsis thaliana chloroplast proteome reveals pathway abundance and novel protein functions.拟南芥叶绿体蛋白质组揭示了途径丰度和新的蛋白质功能。
茉莉酸甲酯作为一种分子开关，促进了用于修饰植物中蛋白质的类异戊二烯骨架生物合成途径之间的相互作用。
Plants (Basel). 2024 Apr 16;13(8):1110. doi: 10.3390/plants13081110.
4
Sparse Reduced Rank Huber Regression in High Dimensions.高维稀疏降秩Huber回归
J Am Stat Assoc. 2023;118(544):2383-2393. doi: 10.1080/01621459.2022.2050243. Epub 2022 Apr 15.
5
Transcription factor CsTT8 promotes fruit coloration by positively regulating the methylerythritol 4-phosphate pathway and carotenoid biosynthesis pathway in citrus ( spp.).转录因子CsTT8通过正向调控柑橘中的甲基赤藓糖醇4-磷酸途径和类胡萝卜素生物合成途径来促进果实着色。
Hortic Res. 2023 Oct 10;10(11):uhad199. doi: 10.1093/hr/uhad199. eCollection 2023 Nov.
6
DRAGON: Determining Regulatory Associations using Graphical models on multi-Omic Networks.DRAGON：基于多组学网络的图形模型确定调控关系。
Nucleic Acids Res. 2023 Feb 22;51(3):e15. doi: 10.1093/nar/gkac1157.
7
Isoprenoid biosynthesis regulation in poplars by methylerythritol phosphate and mevalonic acid pathways.杨树中磷酸甲基赤藓糖醇和甲羟戊酸途径对类异戊二烯生物合成的调控
Front Plant Sci. 2022 Sep 30;13:968780. doi: 10.3389/fpls.2022.968780. eCollection 2022.
8
Metabolomic Profiling in Combination with Data Association Analysis Provide Insights about Potential Metabolic Regulation Networks among Non-Volatile and Volatile Metabolites in .代谢组学分析结合数据关联分析为[具体对象]中非挥发性和挥发性代谢物之间潜在的代谢调控网络提供了见解。
Plants (Basel). 2022 Sep 28;11(19):2557. doi: 10.3390/plants11192557.
9
An overview of heavy-tail extensions of multivariate Gaussian distribution and their relations.多元高斯分布的重尾扩展及其关系概述。
J Appl Stat. 2022 Mar 2;49(13):3477-3494. doi: 10.1080/02664763.2022.2044018. eCollection 2022.
10
Regression-Based Bayesian Estimation and Structure Learning for Nonparanormal Graphical Models.基于回归的非正态图形模型的贝叶斯估计与结构学习
Stat Anal Data Min. 2022 Oct;15(5):611-629. doi: 10.1002/sam.11576. Epub 2022 Feb 28.
Curr Biol. 2004 Mar 9;14(5):354-62. doi: 10.1016/j.cub.2004.02.039.
4
Distinct light-mediated pathways regulate the biosynthesis and exchange of isoprenoid precursors during Arabidopsis seedling development.不同的光介导途径在拟南芥幼苗发育过程中调节类异戊二烯前体的生物合成和交换。
Plant Cell. 2004 Jan;16(1):144-56. doi: 10.1105/tpc.016204. Epub 2003 Dec 5.
5
Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae.酿酒酵母代谢网络中的转录调控原理。
Nat Biotechnol. 2004 Jan;22(1):86-92. doi: 10.1038/nbt918. Epub 2003 Nov 30.
6
Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks.利用动态贝叶斯网络从微阵列实验推断基因调控相互作用的敏感性和特异性。
Bioinformatics. 2003 Nov 22;19(17):2271-82. doi: 10.1093/bioinformatics/btg313.
7
MGraph: graphical models for microarray data analysis.MGraph：用于微阵列数据分析的图形模型。
Bioinformatics. 2003 Nov 22;19(17):2210-1. doi: 10.1093/bioinformatics/btg298.
8
A Bayesian networks approach for predicting protein-protein interactions from genomic data.一种用于从基因组数据预测蛋白质-蛋白质相互作用的贝叶斯网络方法。
Science. 2003 Oct 17;302(5644):449-53. doi: 10.1126/science.1087361.
9
Long-term region-wide declines in Caribbean corals.加勒比地区珊瑚长期区域性衰退。
Science. 2003 Aug 15;301(5635):958-60. doi: 10.1126/science.1086050. Epub 2003 Jul 17.
10
Metabolic cross talk between cytosolic and plastidial pathways of isoprenoid biosynthesis: unidirectional transport of intermediates across the chloroplast envelope membrane.类异戊二烯生物合成的胞质溶胶和质体途径之间的代谢串扰：中间体跨叶绿体包膜单向运输。
Arch Biochem Biophys. 2003 Jul 15;415(2):146-54. doi: 10.1016/s0003-9861(03)00233-9.