Supporting data for "Multi-omics Visualization Platform: An extensible Galaxy plug-in for multi-omics data visualization and exploration"

Proteogenomics integrates genomics, transcriptomics and mass spectrometry (MS)- based proteomics data to identify novel protein sequences arising from gene and transcript sequence variants. Proteogenomic data analysis requires integration of disparate omic software tools, as well as customized tools to view and interpret results. The flexible Galaxy platform has proven valuable for proteogenomic data analysis. Here, we describe a novel Multi-omics Visualization Platform (MVP) for organizing, visualizing and exploring proteogenomic results, adding a critically needed tool for data exploration and interpretation.<br>MVP is built as an HTML Galaxy plugin, primarily based on Javascript. Via the Galaxy API, MVP uses SQlite databases as input -- a custom datatype (mzSQlite) containing MS-based peptide identification information, a variant annotation table, and a coding sequence table. Users can interactively filter identified peptides based on sequence and data quality metrics, view annotated peptide MS data, visualize protein-level information, along with genomic coordinates. Peptides that pass the user-defined thresholds can be sent back to Galaxy via the API for further analysis; processed data and visualizations can also be saved and shared. MVP leverages the Integrated Genomics Viewer JavaScript (IGVjs) framework, enabling interactive visualization of peptides and corresponding transcript and genomic coding information within the MVP interface.<br>MVP provides a powerful, extensible platform for automated, interactive visualization of proteogenomics results within the Galaxy environment, adding a unique and critically needed tool for empowering exploration and interpretation of results. The platform is extensible, providing a basis for further development of new functionalities for proteogenomic data visualization.

蛋白质基因组学（Proteogenomics）整合基因组学、转录组学与基于质谱（Mass Spectrometry，MS）的蛋白质组学数据，以识别由基因及转录本序列变异产生的新型蛋白质序列。蛋白质组学数据分析需整合多种异构组学软件工具，同时还需定制化工具以实现结果的查看与解读。灵活的Galaxy平台已被证实可有效助力蛋白质组学数据分析。本文介绍一款新型多组学可视化平台（Multi-omics Visualization Platform，MVP），用于对蛋白质组学分析结果进行组织、可视化与探索，填补了当前数据探索与解读领域亟需的工具空白。
MVP作为一款基于HTML的Galaxy插件开发，核心依赖Javascript语言。通过Galaxy应用程序编程接口（Application Programming Interface，API），MVP以SQlite数据库作为输入数据源，包含三类数据：一类为包含基于质谱的肽段鉴定信息的自定义数据类型（mzSQlite），另一类为变异注释表，还有一类为编码序列表。用户可基于序列与数据质量指标对已鉴定的肽段进行交互式筛选，查看带注释的肽段质谱数据，同时可视化蛋白质层面信息及基因组坐标。符合用户自定义阈值的肽段可通过API回传至Galaxy平台以进行后续分析；处理后的数据与可视化结果同样支持保存与共享。MVP采用整合基因组查看器JavaScript版（Integrated Genomics Viewer JavaScript，IGVjs）框架，可在MVP界面内实现肽段及其对应转录本与基因组编码信息的交互式可视化。
MVP为Galaxy环境下的蛋白质组学分析结果提供了一款功能强大且可扩展的自动化交互式可视化平台，填补了当前领域内亟需的独特工具空白，助力研究人员对分析结果进行探索与解读。该平台具备良好的可扩展性，可为蛋白质组学数据可视化相关新功能的后续开发提供基础支撑。