Making proteomics accessible: RokaiXplorer for interactive analysis of phospho-proteomic data.

IF 2.4 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY
Bioinformatics advances Pub Date : 2024-06-20 eCollection Date: 2024-01-01 DOI:10.1093/bioadv/vbae077
Serhan Yılmaz, Filipa Blasco Tavares Pereira Lopes, Daniela Schlatzer, Marzieh Ayati, Mark R Chance, Mehmet Koyutürk
{"title":"Making proteomics accessible: RokaiXplorer for interactive analysis of phospho-proteomic data.","authors":"Serhan Yılmaz, Filipa Blasco Tavares Pereira Lopes, Daniela Schlatzer, Marzieh Ayati, Mark R Chance, Mehmet Koyutürk","doi":"10.1093/bioadv/vbae077","DOIUrl":null,"url":null,"abstract":"<p><strong>Summary: </strong>We present RokaiXplorer, an intuitive web tool designed to address the scarcity of user-friendly solutions for proteomics and phospho-proteomics data analysis and visualization. RokaiXplorer streamlines data processing, analysis, and visualization through an interactive online interface, making it accessible to researchers without specialized training in proteomics or data science. With its comprehensive suite of modules, RokaiXplorer facilitates phospho-proteomic analysis at the level of phosphosites, proteins, kinases, biological processes, and pathways. The tool offers functionalities such as data normalization, statistical testing, activity inference, pathway enrichment, subgroup analysis, automated report generation, and multiple visualizations, including volcano plots, bar plots, heat maps, and network views. As a unique feature, RokaiXplorer allows researchers to effortlessly deploy their own data browsers, enabling interactive sharing of research data and findings. Overall, RokaiXplorer fills an important gap in phospho-proteomic data analysis by providing the ability to comprehensively analyze data at multiple levels within a single application.</p><p><strong>Availability and implementation: </strong>Access RokaiXplorer at: http://explorer.rokai.io.</p>","PeriodicalId":72368,"journal":{"name":"Bioinformatics advances","volume":null,"pages":null},"PeriodicalIF":2.4000,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11415779/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Bioinformatics advances","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1093/bioadv/vbae077","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/1/1 0:00:00","PubModel":"eCollection","JCR":"Q2","JCRName":"MATHEMATICAL & COMPUTATIONAL BIOLOGY","Score":null,"Total":0}
引用次数: 0

Abstract

Summary: We present RokaiXplorer, an intuitive web tool designed to address the scarcity of user-friendly solutions for proteomics and phospho-proteomics data analysis and visualization. RokaiXplorer streamlines data processing, analysis, and visualization through an interactive online interface, making it accessible to researchers without specialized training in proteomics or data science. With its comprehensive suite of modules, RokaiXplorer facilitates phospho-proteomic analysis at the level of phosphosites, proteins, kinases, biological processes, and pathways. The tool offers functionalities such as data normalization, statistical testing, activity inference, pathway enrichment, subgroup analysis, automated report generation, and multiple visualizations, including volcano plots, bar plots, heat maps, and network views. As a unique feature, RokaiXplorer allows researchers to effortlessly deploy their own data browsers, enabling interactive sharing of research data and findings. Overall, RokaiXplorer fills an important gap in phospho-proteomic data analysis by providing the ability to comprehensively analyze data at multiple levels within a single application.

Availability and implementation: Access RokaiXplorer at: http://explorer.rokai.io.

让蛋白质组学变得触手可及:用于交互式分析磷酸蛋白组数据的 RokaiXplorer。
摘要:我们介绍的 RokaiXplorer 是一种直观的网络工具,旨在解决蛋白质组学和磷酸化蛋白质组学数据分析和可视化方面缺乏用户友好型解决方案的问题。RokaiXplorer 通过交互式在线界面简化了数据处理、分析和可视化过程,使没有接受过蛋白质组学或数据科学专业培训的研究人员也能使用。RokaiXplorer 拥有一套全面的模块,有助于在磷酸位点、蛋白质、激酶、生物过程和通路水平上进行磷酸蛋白组学分析。该工具提供的功能包括数据归一化、统计测试、活性推断、通路富集、亚组分析、自动报告生成和多种可视化,包括火山图、柱状图、热图和网络视图。作为一项独特功能,RokaiXplorer 允许研究人员毫不费力地部署自己的数据浏览器,从而实现研究数据和结果的互动共享。总之,RokaiXplorer 通过在单个应用程序中提供多层次综合数据分析能力,填补了磷酸蛋白组数据分析领域的重要空白:访问 RokaiXplorer:http://explorer.rokai.io。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 求助全文
来源期刊
CiteScore
1.60
自引率
0.00%
发文量
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信