DGE-ontology：快速简单的基因组富集分析和可视化工具

IF 2.4 4区计算机科学 Q2 COMPUTER SCIENCE, SOFTWARE ENGINEERING

SoftwareX Pub Date : 2024-10-04 DOI:10.1016/j.softx.2024.101899

Michal Bukowski, Benedykt Wladyka

{"title":"DGE-ontology：快速简单的基因组富集分析和可视化工具","authors":"Michal Bukowski, Benedykt Wladyka","doi":"10.1016/j.softx.2024.101899","DOIUrl":null,"url":null,"abstract":"<div><div>High-throughput quantification techniques provide considerable amounts of data. Making sense of such data requires not only thorough statistical analysis but a logical approach to data visualisation. DGE-ontology is software that has been primarily designed for transcriptomics, however it may be utilised for any data that express fold change of relative or absolute quantity measures of multiple entities, such as transcripts, proteins or metabolites. The software integrates results of differential and functional analyses in order to produce a single circular, highly informative and visually appealing chart. The chart simultaneously depicts numbers of quantified entities, their assignment to functional categories, singles out statistically over-represented categories, and visualises quantity fold change values. The presented approach to data visualisation considerably facilitates communication of experimental results as well as inference from large omic data sets.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"28 ","pages":"Article 101899"},"PeriodicalIF":2.4000,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"DGE-ontology: A quick and simple gene set enrichment analysis and visualisation tool\",\"authors\":\"Michal Bukowski, Benedykt Wladyka\",\"doi\":\"10.1016/j.softx.2024.101899\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><div>High-throughput quantification techniques provide considerable amounts of data. Making sense of such data requires not only thorough statistical analysis but a logical approach to data visualisation. DGE-ontology is software that has been primarily designed for transcriptomics, however it may be utilised for any data that express fold change of relative or absolute quantity measures of multiple entities, such as transcripts, proteins or metabolites. The software integrates results of differential and functional analyses in order to produce a single circular, highly informative and visually appealing chart. The chart simultaneously depicts numbers of quantified entities, their assignment to functional categories, singles out statistically over-represented categories, and visualises quantity fold change values. The presented approach to data visualisation considerably facilitates communication of experimental results as well as inference from large omic data sets.</div></div>\",\"PeriodicalId\":21905,\"journal\":{\"name\":\"SoftwareX\",\"volume\":\"28 \",\"pages\":\"Article 101899\"},\"PeriodicalIF\":2.4000,\"publicationDate\":\"2024-10-04\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"SoftwareX\",\"FirstCategoryId\":\"94\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S2352711024002693\",\"RegionNum\":4,\"RegionCategory\":\"计算机科学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"COMPUTER SCIENCE, SOFTWARE ENGINEERING\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"SoftwareX","FirstCategoryId":"94","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S2352711024002693","RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"COMPUTER SCIENCE, SOFTWARE ENGINEERING","Score":null,"Total":0}

引用次数: 0

摘要

高通量定量技术可提供大量数据。要理解这些数据，不仅需要全面的统计分析，还需要合理的数据可视化方法。DGE-ontology 软件主要是为转录组学设计的，但也可用于任何表达转录本、蛋白质或代谢物等多个实体的相对或绝对数量测量值折叠变化的数据。该软件整合了差异分析和功能分析的结果，以生成一个单一的、信息量大、视觉效果好的圆形图表。该图表同时描述了量化实体的数量、它们被分配到的功能类别、挑选出统计上代表性过高的类别，并可视化数量折叠变化值。所介绍的数据可视化方法大大促进了实验结果的交流以及大型 omic 数据集的推断。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

查看原文本刊更多论文

DGE-ontology: A quick and simple gene set enrichment analysis and visualisation tool

High-throughput quantification techniques provide considerable amounts of data. Making sense of such data requires not only thorough statistical analysis but a logical approach to data visualisation. DGE-ontology is software that has been primarily designed for transcriptomics, however it may be utilised for any data that express fold change of relative or absolute quantity measures of multiple entities, such as transcripts, proteins or metabolites. The software integrates results of differential and functional analyses in order to produce a single circular, highly informative and visually appealing chart. The chart simultaneously depicts numbers of quantified entities, their assignment to functional categories, singles out statistically over-represented categories, and visualises quantity fold change values. The presented approach to data visualisation considerably facilitates communication of experimental results as well as inference from large omic data sets.

求助全文

通过发布文献求助，成功后即可免费获取论文全文。去求助

来源期刊

SoftwareX COMPUTER SCIENCE, SOFTWARE ENGINEERING-

CiteScore

5.50

自引率

2.90%

发文量

184

审稿时长

9 weeks

期刊介绍： SoftwareX aims to acknowledge the impact of software on today''s research practice, and on new scientific discoveries in almost all research domains. SoftwareX also aims to stress the importance of the software developers who are, in part, responsible for this impact. To this end, SoftwareX aims to support publication of research software in such a way that: The software is given a stamp of scientific relevance, and provided with a peer-reviewed recognition of scientific impact; The software developers are given the credits they deserve; The software is citable, allowing traditional metrics of scientific excellence to apply; The academic career paths of software developers are supported rather than hindered; The software is publicly available for inspection, validation, and re-use. Above all, SoftwareX aims to inform researchers about software applications, tools and libraries with a (proven) potential to impact the process of scientific discovery in various domains. The journal is multidisciplinary and accepts submissions from within and across subject domains such as those represented within the broad thematic areas below: Mathematical and Physical Sciences; Environmental Sciences; Medical and Biological Sciences; Humanities, Arts and Social Sciences. Originating from these broad thematic areas, the journal also welcomes submissions of software that works in cross cutting thematic areas, such as citizen science, cybersecurity, digital economy, energy, global resource stewardship, health and wellbeing, etcetera. SoftwareX specifically aims to accept submissions representing domain-independent software that may impact more than one research domain.