Multi-omics Visualization Platform: An extensible Galaxy plug-in for multi-omics data visualization and exploration
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Abstract
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.
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Now published in GigaScience doi: 10.1093/gigascience/giaa025
Thomas McGowan 1Minnesota Supercomputing Institute, University of Minnesota, 599 Walter Library, 117 Pleasant Street SE, Minneapolis, MN 55455Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteJames E. Johnson 1Minnesota Supercomputing Institute, University of Minnesota, 599 Walter Library, 117 Pleasant Street SE, Minneapolis, MN 55455Find this author on Google ScholarFind this author on PubMedSearch for this author on this sitePraveen Kumar 2Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 554553Bioinformatics and Computational Biology program, University of Minnesota-Rochester, 111 South Broadway, Suite 300, Rochester, MN 55904Find this …
Now published in GigaScience doi: 10.1093/gigascience/giaa025
Thomas McGowan 1Minnesota Supercomputing Institute, University of Minnesota, 599 Walter Library, 117 Pleasant Street SE, Minneapolis, MN 55455Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteJames E. Johnson 1Minnesota Supercomputing Institute, University of Minnesota, 599 Walter Library, 117 Pleasant Street SE, Minneapolis, MN 55455Find this author on Google ScholarFind this author on PubMedSearch for this author on this sitePraveen Kumar 2Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 554553Bioinformatics and Computational Biology program, University of Minnesota-Rochester, 111 South Broadway, Suite 300, Rochester, MN 55904Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteRay Sajulga 2Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteSubina Mehta 2Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455Find this author on Google ScholarFind this author on PubMedSearch for this author on this sitePratik D. Jagtap 2Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteTimothy J. Griffin 2Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: tgriffin@umn.edu
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa025 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102152 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102153
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