{"title":"Clust&See3.0 : clustering, module exploration and annotation.","authors":"Fabrice Lopez, Lionel Spinelli, Christine Brun","doi":"10.12688/f1000research.152711.1","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>Cytoscape is an open-source software to visualize and analyze networks. However, large networks, such as protein interaction networks, are still difficult to analyze as a whole.</p><p><strong>Methods: </strong>Here, we propose Clust&See3.0, a novel version of a Cytoscape app that has been developed to identify, visualize and manipulate network clusters and modules. It is now enriched with functionalities allowing custom annotations of nodes and computation of their statistical enrichments.</p><p><strong>Results: </strong>As the wealth of multi-omics data is growing, such functionalities are highly valuable for a better understanding of biological module composition, as illustrated by the presented use case.</p><p><strong>Conclusions: </strong>In summary, the originality of Clust&See3.0 lies in providing users with a complete tool for network clusters analyses: from cluster identification, visualization, node and cluster annotations to annotation statistical analyses.</p>","PeriodicalId":12260,"journal":{"name":"F1000Research","volume":"13 ","pages":"994"},"PeriodicalIF":0.0000,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11528184/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"F1000Research","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.12688/f1000research.152711.1","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/1/1 0:00:00","PubModel":"eCollection","JCR":"Q2","JCRName":"Pharmacology, Toxicology and Pharmaceutics","Score":null,"Total":0}
引用次数: 0
Abstract
Background: Cytoscape is an open-source software to visualize and analyze networks. However, large networks, such as protein interaction networks, are still difficult to analyze as a whole.
Methods: Here, we propose Clust&See3.0, a novel version of a Cytoscape app that has been developed to identify, visualize and manipulate network clusters and modules. It is now enriched with functionalities allowing custom annotations of nodes and computation of their statistical enrichments.
Results: As the wealth of multi-omics data is growing, such functionalities are highly valuable for a better understanding of biological module composition, as illustrated by the presented use case.
Conclusions: In summary, the originality of Clust&See3.0 lies in providing users with a complete tool for network clusters analyses: from cluster identification, visualization, node and cluster annotations to annotation statistical analyses.
F1000ResearchPharmacology, Toxicology and Pharmaceutics-Pharmacology, Toxicology and Pharmaceutics (all)
CiteScore
5.00
自引率
0.00%
发文量
1646
审稿时长
1 weeks
期刊介绍：
F1000Research publishes articles and other research outputs reporting basic scientific, scholarly, translational and clinical research across the physical and life sciences, engineering, medicine, social sciences and humanities. F1000Research is a scholarly publication platform set up for the scientific, scholarly and medical research community; each article has at least one author who is a qualified researcher, scholar or clinician actively working in their speciality and who has made a key contribution to the article. Articles must be original (not duplications). All research is suitable irrespective of the perceived level of interest or novelty; we welcome confirmatory and negative results, as well as null studies. F1000Research publishes different type of research, including clinical trials, systematic reviews, software tools, method articles, and many others. Reviews and Opinion articles providing a balanced and comprehensive overview of the latest discoveries in a particular field, or presenting a personal perspective on recent developments, are also welcome. See the full list of article types we accept for more information.
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