TY - JOUR
T1 - Multi-omics Visualization Platform
T2 - An extensible Galaxy plug-in for multi-omics data visualization and exploration
AU - Mcgowan, Thomas
AU - Johnson, James E.
AU - Kumar, Praveen
AU - Sajulga, Ray
AU - Mehta, Subina
AU - Jagtap, Pratik D.
AU - Griffin, Timothy J.
N1 - Funding Information:
This work was funded in part by National Institutes of Health/National Cancer Institute grant U24CA199347 to Dr. Griffin and the Galaxy-P team.
Publisher Copyright:
© 2020 The Author(s) 2020.
PY - 2020/4/6
Y1 - 2020/4/6
N2 - Background: 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. Findings: MVP is built as an HTML Galaxy plug-in, primarily based on JavaScript. Via the Galaxy API, MVP uses SQLite databases as input - a custom data type (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, and 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 framework, enabling interactive visualization of peptides and corresponding transcript and genomic coding information within the MVP interface. Conclusions: MVP provides a powerful, extensible platform for automated, interactive visualization of proteogenomic 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.
AB - Background: 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. Findings: MVP is built as an HTML Galaxy plug-in, primarily based on JavaScript. Via the Galaxy API, MVP uses SQLite databases as input - a custom data type (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, and 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 framework, enabling interactive visualization of peptides and corresponding transcript and genomic coding information within the MVP interface. Conclusions: MVP provides a powerful, extensible platform for automated, interactive visualization of proteogenomic 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.
KW - Galaxy
KW - Integrated Genomics Viewer
KW - RNA-Seq
KW - mass spectrometry
KW - proteogenomics
KW - proteomics
KW - transcriptomics
KW - visualization
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U2 - 10.1093/gigascience/giaa025
DO - 10.1093/gigascience/giaa025
M3 - Article
C2 - 32236523
AN - SCOPUS:85082792753
SN - 2047-217X
VL - 9
JO - GigaScience
JF - GigaScience
IS - 4
M1 - giaa025
ER -