Dataset Information

SBGNview: towards data analysis, integration and visualization on all pathways.

ABSTRACT:

Summary

Pathway analysis is widely used in genomics and omics research, but the data visualization has been highly limited in function, pathway coverage and data format. Here, we develop SBGNview a comprehensive R package to address these needs. By adopting the standard SBGN format, SBGNview greatly extend the coverage of pathway-based analysis and data visualization to essentially all major pathway databases beyond KEGG, including 5200 reference pathways and over 3000 species. In addition, SBGNview substantially extends or exceeds current tools (esp. Pathview) in both design and function, including standard input format (SBGN), high-quality output graphics (SVG format) convenient for both interpretation and further update, and flexible and open-end workflow for iterative editing and interactive visualization (Highlighter module). In addition to pathway analysis and data visualization, SBGNview provides essential infrastructure for SBGN data manipulation and processing.

Availability and implementation

The data underlying this article are available as part of the SBGNview package is available on both GitHub and Bioconductor: https://github.com/datapplab/SBGNview, https://bioconductor.org/packages/SBGNview.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Dong X

PROVIDER: S-EPMC8826166 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature

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Publications

SBGNview: towards data analysis, integration and visualization on all pathways.

Dong Xiaoxi X Vegesna Kovidh K Brouwer Cory C Luo Weijun W

Bioinformatics (Oxford, England) 20220201 5

<h4>Summary</h4>Pathway analysis is widely used in genomics and omics research, but the data visualization has been highly limited in function, pathway coverage and data format. Here, we develop SBGNview a comprehensive R package to address these needs. By adopting the standard SBGN format, SBGNview greatly extend the coverage of pathway-based analysis and data visualization to essentially all major pathway databases beyond KEGG, including 5200 reference pathways and over 3000 species. In additi ...[more]

PMID: 34864890

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Project description:BACKGROUND:Bioinformatics research for finding biological mechanisms can be done by analysis of transcriptome data with pathway based interpretation. Therefore, researchers have tried to develop tools to analyze transcriptome data with pathway based interpretation. Over the years, the amount of omics data has become huge, e.g., TCGA, and the data types to be analyzed have come in many varieties, including mutations, copy number variations, and transcriptome. We also need to consider a complex relationship with regulators of genes, particularly Transcription Factors(TF). However, there has not been a system for pathway based exploration and analysis of TCGA multi-omics data. In this reason, We have developed a web based system BRCA-Pathway to fulfill the need for pathway based analysis of TCGA multi-omics data. RESULTS:BRCA-Pathway is a structured integration and visual exploration system of TCGA breast cancer data on KEGG pathways. For data integration, a relational database is designed and used to integrate multi-omics data of TCGA-BRCA, KEGG pathway data, Hallmark gene sets, transcription factors, driver genes, and PAM50 subtypes. For data exploration, multi-omics data such as SNV, CNV and gene expression can be visualized simultaneously in KEGG pathway maps, together with transcription factors-target genes (TF-TG) correlation and relationships among cancer driver genes. In addition, 'Pathways summary' and 'Oncoprint' with mutual exclusivity sort can be generated dynamically with a request by the user. Data in BRCA-Pathway can be downloaded by REST API for further analysis. CONCLUSIONS:BRCA-Pathway helps researchers navigate omics data towards potentially important genes, regulators, and discover complex patterns involving mutations, CNV, and gene expression data of various patient groups in the biological pathway context. In addition, mutually exclusive genomic alteration patterns in a specific pathway can be generated. BRCA-Pathway can provide an integrative perspective on the breast cancer omics data, which can help researchers discover new insights on the biological mechanisms of breast cancer.

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Dataset Information

SBGNview: towards data analysis, integration and visualization on all pathways.

Summary

Availability and implementation

Supplementary information

Publications

SBGNview: towards data analysis, integration and visualization on all pathways.

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