• 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

Orthoscape：一款基于分类学和同源性原理对基于KEGG的基因网络进行分组和可视化的Cytoscape应用程序。

Orthoscape: a cytoscape application for grouping and visualization KEGG based gene networks by taxonomy and homology principles.

作者信息

Mustafin Zakhar Sergeevich, Lashin Sergey Alexandrovich, Matushkin Yury Georgievich, Gunbin Konstantin Vladimirovich, Afonnikov Dmitry Arkadievich

机构信息

Institute of Cytology and Genetics SB RAS, Lavrentiev Avenue 10, Novosibirsk, 630090, Russia.

Novosibirsk State University, Pirogova st. 2, Novosibirsk, 630090, Russia.

出版信息

BMC Bioinformatics. 2017 Jan 27;18(Suppl 1):1427. doi: 10.1186/s12859-016-1427-5.

DOI:10.1186/s12859-016-1427-5
PMID:28466792
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5333177/
Abstract

BACKGROUND

There are many available software tools for visualization and analysis of biological networks. Among them, Cytoscape ( http://cytoscape.org/ ) is one of the most comprehensive packages, with many plugins and applications which extends its functionality by providing analysis of protein-protein interaction, gene regulatory and gene co-expression networks, metabolic, signaling, neural as well as ecological-type networks including food webs, communities networks etc. Nevertheless, only three plugins tagged 'network evolution' found in Cytoscape official app store and in literature. We have developed a new Cytoscape 3.0 application Orthoscape aimed to facilitate evolutionary analysis of gene networks and visualize the results.

RESULTS

Orthoscape aids in analysis of evolutionary information available for gene sets and networks by highlighting: (1) the orthology relationships between genes; (2) the evolutionary origin of gene network components; (3) the evolutionary pressure mode (diversifying or stabilizing, negative or positive selection) of orthologous groups in general and/or branch-oriented mode. The distinctive feature of Orthoscape is the ability to control all data analysis steps via user-friendly interface.

CONCLUSION

Orthoscape allows its users to analyze gene networks or separated gene sets in the context of evolution. At each step of data analysis, Orthoscape also provides for convenient visualization and data manipulation.

摘要

背景

有许多可用的软件工具用于生物网络的可视化和分析。其中，Cytoscape（http://cytoscape.org/）是最全面的软件包之一，它有许多插件和应用程序，通过提供蛋白质-蛋白质相互作用、基因调控和基因共表达网络、代谢、信号传导、神经以及包括食物网、群落网络等在内的生态型网络的分析来扩展其功能。然而，在Cytoscape官方应用商店和文献中仅发现三个标记为“网络进化”的插件。我们开发了一个新的Cytoscape 3.0应用程序Orthoscape，旨在促进基因网络的进化分析并可视化结果。

结果

Orthoscape通过突出显示以下内容来辅助分析基因集和网络的进化信息：（1）基因之间的直系同源关系；（2）基因网络组件的进化起源；（3）直系同源组的进化压力模式（多样化或稳定化、负选择或正选择），总体上和/或以分支导向模式。Orthoscape的独特之处在于能够通过用户友好的界面控制所有数据分析步骤。

结论

Orthoscape允许用户在进化背景下分析基因网络或分离的基因集。在数据分析的每个步骤中，Orthoscape还提供方便的可视化和数据操作。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eb46/5333177/a7c3e3b26d1c/12859_2016_1427_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eb46/5333177/f263dc2db67c/12859_2016_1427_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eb46/5333177/3faad392f086/12859_2016_1427_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eb46/5333177/808ee114c0ce/12859_2016_1427_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eb46/5333177/bc3adc65c99d/12859_2016_1427_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eb46/5333177/2ba4674a187d/12859_2016_1427_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eb46/5333177/9359af9a5909/12859_2016_1427_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eb46/5333177/15873ba38c68/12859_2016_1427_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eb46/5333177/a7c3e3b26d1c/12859_2016_1427_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eb46/5333177/f263dc2db67c/12859_2016_1427_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eb46/5333177/3faad392f086/12859_2016_1427_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eb46/5333177/808ee114c0ce/12859_2016_1427_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eb46/5333177/bc3adc65c99d/12859_2016_1427_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eb46/5333177/2ba4674a187d/12859_2016_1427_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eb46/5333177/9359af9a5909/12859_2016_1427_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eb46/5333177/15873ba38c68/12859_2016_1427_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eb46/5333177/a7c3e3b26d1c/12859_2016_1427_Fig8_HTML.jpg

相似文献

1
Orthoscape: a cytoscape application for grouping and visualization KEGG based gene networks by taxonomy and homology principles.Orthoscape：一款基于分类学和同源性原理对基于KEGG的基因网络进行分组和可视化的Cytoscape应用程序。
BMC Bioinformatics. 2017 Jan 27;18(Suppl 1):1427. doi: 10.1186/s12859-016-1427-5.
2
Development and use of a Cytoscape app for GRNCOP2.开发并使用 Cytoscape 应用程序进行 GRNCOP2。
Comput Methods Programs Biomed. 2019 Aug;177:211-218. doi: 10.1016/j.cmpb.2019.05.030. Epub 2019 Jun 4.
3
GNC-app: A new Cytoscape app to rate gene networks biological coherence using gene-gene indirect relationships.GNC应用程序：一种用于利用基因-基因间接关系对基因网络生物学连贯性进行评分的新型Cytoscape应用程序。
Biosystems. 2018 Apr;166:61-65. doi: 10.1016/j.biosystems.2018.01.007. Epub 2018 Feb 14.
4
CytoASP: a Cytoscape app for qualitative consistency reasoning, prediction and repair in biological networks.CytoASP：一款用于生物网络中定性一致性推理、预测和修复的Cytoscape应用程序。
BMC Syst Biol. 2015 Jul 11;9:34. doi: 10.1186/s12918-015-0179-6.
5
Cytoscape: a community-based framework for network modeling.Cytoscape：一个基于社区的网络建模框架。
Methods Mol Biol. 2009;563:219-39. doi: 10.1007/978-1-60761-175-2_12.
6
DisGeNET: a Cytoscape plugin to visualize, integrate, search and analyze gene-disease networks.DisGeNET：一个 Cytoscape 插件，用于可视化、集成、搜索和分析基因-疾病网络。
Bioinformatics. 2010 Nov 15;26(22):2924-6. doi: 10.1093/bioinformatics/btq538. Epub 2010 Sep 21.
7
SpotXplore: a Cytoscape plugin for visual exploration of hotspot expression in gene regulatory networks.SpotXplore：一个 Cytoscape 的插件，用于可视化探索基因调控网络中的热点表达。
Bioinformatics. 2010 Nov 15;26(22):2922-3. doi: 10.1093/bioinformatics/btq535. Epub 2010 Sep 21.
8
Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data.Cytoscape StringApp：蛋白质组学数据的网络分析和可视化。
J Proteome Res. 2019 Feb 1;18(2):623-632. doi: 10.1021/acs.jproteome.8b00702. Epub 2018 Dec 5.
9
CytoITMprobe: a network information flow plugin for Cytoscape.CytoITMprobe：一款用于Cytoscape的网络信息流插件。
BMC Res Notes. 2012 May 15;5:237. doi: 10.1186/1756-0500-5-237.
10
Linking Cytoscape and the corynebacterial reference database CoryneRegNet.将Cytoscape与棒状杆菌参考数据库CoryneRegNet相连接。
BMC Genomics. 2008 Apr 21;9:184. doi: 10.1186/1471-2164-9-184.

引用本文的文献

1
Candidate SNP Markers Significantly Altering the Affinity of the TATA-Binding Protein for the Promoters of Human Genes Associated with Primary Open-Angle Glaucoma.候选单核苷酸多态性标记显著改变TATA结合蛋白与原发性开角型青光眼相关人类基因启动子的亲和力。
Int J Mol Sci. 2024 Nov 28;25(23):12802. doi: 10.3390/ijms252312802.
2
Bioinformatic Analysis Reveals the Role of Translation Elongation Efficiency Optimisation in the Evolution of Genus.生物信息学分析揭示了翻译延伸效率优化在该属进化中的作用。
Biology (Basel). 2023 Oct 16;12(10):1338. doi: 10.3390/biology12101338.
3
Candidate SNP Markers Significantly Altering the Affinity of TATA-Binding Protein for the Promoters of Human Hub Genes for Atherogenesis, Atherosclerosis and Atheroprotection.

本文引用的文献

1
Pathways on demand: automated reconstruction of human signaling networks.按需构建通路：人类信号网络的自动重建
NPJ Syst Biol Appl. 2016 Mar 3;2:16002. doi: 10.1038/npjsba.2016.2. eCollection 2016.
2
CoExpNetViz: Comparative Co-Expression Networks Construction and Visualization Tool.CoExpNetViz：比较共表达网络构建与可视化工具。
Front Plant Sci. 2016 Jan 5;6:1194. doi: 10.3389/fpls.2015.01194. eCollection 2015.
3
Computing Workflows for Biologists: A Roadmap.生物学家的计算工作流程：路线图
候选单核苷酸多态性标记物显著改变 TATA 结合蛋白与人类动脉粥样硬化、动脉粥样硬化和动脉保护关键基因启动子的亲和力。
Int J Mol Sci. 2023 May 19;24(10):9010. doi: 10.3390/ijms24109010.
4
Differentially Expressed Genes and Molecular Susceptibility to Human Age-Related Diseases.差异表达基因与人类年龄相关性疾病的分子易感性。
Int J Mol Sci. 2023 Feb 16;24(4):3996. doi: 10.3390/ijms24043996.
5
A Streamlined Approach to Pathway Analysis from RNA-Sequencing Data.一种从RNA测序数据进行通路分析的简化方法。
Methods Protoc. 2021 Mar 17;4(1):21. doi: 10.3390/mps4010021.
6
FunHoP: Enhanced Visualization and Analysis of Functionally Homologous Proteins in Complex Metabolic Networks.FunHoP：复杂代谢网络中功能同源蛋白的增强可视化和分析。
Genomics Proteomics Bioinformatics. 2021 Oct;19(5):848-859. doi: 10.1016/j.gpb.2021.03.003. Epub 2021 Mar 17.
7
Nine Genes Mediate the Therapeutic Effects of Iodine-131 Radiotherapy in Thyroid Carcinoma Patients.九种基因介导碘-131 放疗治疗甲状腺癌患者的疗效。
Dis Markers. 2020 Jun 16;2020:9369341. doi: 10.1155/2020/9369341. eCollection 2020.
8
Phylostratigraphic Analysis Shows the Earliest Origination of the Abiotic Stress Associated Genes in .系统发生分析表明，与非生物胁迫相关的基因最早起源于 。
Genes (Basel). 2019 Nov 22;10(12):963. doi: 10.3390/genes10120963.
9
Feifukang ameliorates pulmonary fibrosis by inhibiting JAK-STAT signaling pathway.肺复康通过抑制 JAK-STAT 信号通路改善肺纤维化。
BMC Complement Altern Med. 2018 Aug 9;18(1):234. doi: 10.1186/s12906-018-2297-3.
10
Towards a Dynamic Interaction Network of Life to unify and expand the evolutionary theory.走向生命动态交互网络以统一和拓展进化理论。
BMC Biol. 2018 May 29;16(1):56. doi: 10.1186/s12915-018-0531-6.
PLoS Biol. 2015 Nov 24;13(11):e1002303. doi: 10.1371/journal.pbio.1002303. eCollection 2015.
4
ReNE: a cytoscape plugin for regulatory network enhancement.ReNE：一种用于增强调控网络的Cytoscape插件。
PLoS One. 2014 Dec 26;9(12):e115585. doi: 10.1371/journal.pone.0115585. eCollection 2014.
5
CyKEGGParser: tailoring KEGG pathways to fit into systems biology analysis workflows.CyKEGGParser：定制KEGG通路以适应系统生物学分析工作流程。
F1000Res. 2014 Jul 1;3:145. doi: 10.12688/f1000research.4410.2. eCollection 2014.
6
GASOLINE: a Cytoscape app for multiple local alignment of PPI networks.GASOLINE：一款用于蛋白质-蛋白质相互作用网络多重局部比对的Cytoscape应用程序。
F1000Res. 2014 Jul 1;3:140. doi: 10.12688/f1000research.4537.2. eCollection 2014.
7
Pepper: cytoscape app for protein complex expansion using protein-protein interaction networks.Pepper：用于利用蛋白质-蛋白质相互作用网络扩展蛋白质复合物的Cytoscape应用程序。
Bioinformatics. 2014 Dec 1;30(23):3419-20. doi: 10.1093/bioinformatics/btu517. Epub 2014 Aug 18.
8
MetDisease--connecting metabolites to diseases via literature.MetDisease--通过文献将代谢物与疾病联系起来。
Bioinformatics. 2014 Aug 1;30(15):2239-41. doi: 10.1093/bioinformatics/btu179. Epub 2014 Apr 8.
9
Integrative approaches for finding modular structure in biological networks.综合方法寻找生物网络中的模块结构。
Nat Rev Genet. 2013 Oct;14(10):719-32. doi: 10.1038/nrg3552.
10
Top-down network analysis to drive bottom-up modeling of physiological processes.自上而下的网络分析以推动生理过程的自下而上建模。
J Comput Biol. 2013 May;20(5):409-18. doi: 10.1089/cmb.2012.0274.