Transomics2cytoscape: an automated software for interpretable 2.5-dimensional visualization of trans-omic networks
Abstract Biochemical network visualization is one of the essential technologies for mechanistic interpretation of omics data. In particular, recent advances in multi-omics measurement and analysis require the development of visualization methods that encompass multiple omics data. Visualization in 2...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2024-02-01
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| Series: | npj Systems Biology and Applications |
| Online Access: | https://doi.org/10.1038/s41540-024-00342-8 |
| _version_ | 1797274175911493632 |
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| author | Kozo Nishida Junichi Maruyama Kazunari Kaizu Koichi Takahashi Katsuyuki Yugi |
| author_facet | Kozo Nishida Junichi Maruyama Kazunari Kaizu Koichi Takahashi Katsuyuki Yugi |
| author_sort | Kozo Nishida |
| collection | DOAJ |
| description | Abstract Biochemical network visualization is one of the essential technologies for mechanistic interpretation of omics data. In particular, recent advances in multi-omics measurement and analysis require the development of visualization methods that encompass multiple omics data. Visualization in 2.5 dimension (2.5D visualization), which is an isometric view of stacked X-Y planes, is a convenient way to interpret multi-omics/trans-omics data in the context of the conventional layouts of biochemical networks drawn on each of the stacked omics layers. However, 2.5D visualization of trans-omics networks is a state-of-the-art method that primarily relies on time-consuming human efforts involving manual drawing. Here, we present an R Bioconductor package ‘transomics2cytoscape’ for automated visualization of 2.5D trans-omics networks. We confirmed that transomics2cytoscape could be used for rapid visualization of trans-omics networks presented in published papers within a few minutes. Transomics2cytoscape allows for frequent update/redrawing of trans-omics networks in line with the progress in multi-omics/trans-omics data analysis, thereby enabling network-based interpretation of multi-omics data at each research step. The transomics2cytoscape source code is available at https://github.com/ecell/transomics2cytoscape . |
| first_indexed | 2024-03-07T14:55:38Z |
| format | Article |
| id | doaj.art-8b8b1e72d9724f8a83b379ede954e7e5 |
| institution | Directory Open Access Journal |
| issn | 2056-7189 |
| language | English |
| last_indexed | 2024-03-07T14:55:38Z |
| publishDate | 2024-02-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | npj Systems Biology and Applications |
| spelling | doaj.art-8b8b1e72d9724f8a83b379ede954e7e52024-03-05T19:28:53ZengNature Portfolionpj Systems Biology and Applications2056-71892024-02-011011910.1038/s41540-024-00342-8Transomics2cytoscape: an automated software for interpretable 2.5-dimensional visualization of trans-omic networksKozo Nishida0Junichi Maruyama1Kazunari Kaizu2Koichi Takahashi3Katsuyuki Yugi4Laboratory for Integrated Cellular Systems, RIKEN Center for Integrative Medical SciencesLaboratory for Integrated Cellular Systems, RIKEN Center for Integrative Medical SciencesCenter for Biosystems Dynamics Research (BDR), RIKENCenter for Biosystems Dynamics Research (BDR), RIKENLaboratory for Integrated Cellular Systems, RIKEN Center for Integrative Medical SciencesAbstract Biochemical network visualization is one of the essential technologies for mechanistic interpretation of omics data. In particular, recent advances in multi-omics measurement and analysis require the development of visualization methods that encompass multiple omics data. Visualization in 2.5 dimension (2.5D visualization), which is an isometric view of stacked X-Y planes, is a convenient way to interpret multi-omics/trans-omics data in the context of the conventional layouts of biochemical networks drawn on each of the stacked omics layers. However, 2.5D visualization of trans-omics networks is a state-of-the-art method that primarily relies on time-consuming human efforts involving manual drawing. Here, we present an R Bioconductor package ‘transomics2cytoscape’ for automated visualization of 2.5D trans-omics networks. We confirmed that transomics2cytoscape could be used for rapid visualization of trans-omics networks presented in published papers within a few minutes. Transomics2cytoscape allows for frequent update/redrawing of trans-omics networks in line with the progress in multi-omics/trans-omics data analysis, thereby enabling network-based interpretation of multi-omics data at each research step. The transomics2cytoscape source code is available at https://github.com/ecell/transomics2cytoscape .https://doi.org/10.1038/s41540-024-00342-8 |
| spellingShingle | Kozo Nishida Junichi Maruyama Kazunari Kaizu Koichi Takahashi Katsuyuki Yugi Transomics2cytoscape: an automated software for interpretable 2.5-dimensional visualization of trans-omic networks npj Systems Biology and Applications |
| title | Transomics2cytoscape: an automated software for interpretable 2.5-dimensional visualization of trans-omic networks |
| title_full | Transomics2cytoscape: an automated software for interpretable 2.5-dimensional visualization of trans-omic networks |
| title_fullStr | Transomics2cytoscape: an automated software for interpretable 2.5-dimensional visualization of trans-omic networks |
| title_full_unstemmed | Transomics2cytoscape: an automated software for interpretable 2.5-dimensional visualization of trans-omic networks |
| title_short | Transomics2cytoscape: an automated software for interpretable 2.5-dimensional visualization of trans-omic networks |
| title_sort | transomics2cytoscape an automated software for interpretable 2 5 dimensional visualization of trans omic networks |
| url | https://doi.org/10.1038/s41540-024-00342-8 |
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