OnPLS-based multi-block data integration: a multivariate approach to interrogating biological interactions in asthma
Integration of multiomics data remains a key challenge in fulfilling the potential of comprehensive systems biology. Multiple-block orthogonal projections to latent structures (OnPLS) is a projection method that simultaneously models multiple data matrices, reducing feature space without relying on...
| Main Authors: | , , , , , , , , , , |
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| Format: | Journal article |
| Language: | English |
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American Chemical Society
2018
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| _version_ | 1826289256615641088 |
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| author | Reinke, SN Galindo-Prieto, B Skotare, T Broadhurst, DI Singhania, A Horowitz, D Djukanovic, R Hinks, TSC Geladi, P Trygg, J Wheelock, CE |
| author_facet | Reinke, SN Galindo-Prieto, B Skotare, T Broadhurst, DI Singhania, A Horowitz, D Djukanovic, R Hinks, TSC Geladi, P Trygg, J Wheelock, CE |
| author_sort | Reinke, SN |
| collection | OXFORD |
| description | Integration of multiomics data remains a key challenge in fulfilling the potential of comprehensive systems biology. Multiple-block orthogonal projections to latent structures (OnPLS) is a projection method that simultaneously models multiple data matrices, reducing feature space without relying on a priori biological knowledge. In order to improve the interpretability of OnPLS models, the associated multi-block variable influence on orthogonal projections (MB-VIOP) method is used to identify variables with the highest contribution to the model. This study combined OnPLS and MB-VIOP with interactive visualization methods to interrogate an exemplar multiomics study, using a subset of 22 individuals from an asthma cohort. Joint data structure in six data blocks was assessed: transcriptomics; metabolomics; targeted assays for sphingolipids, oxylipins, and fatty acids; and a clinical block including lung function, immune cell differentials, and cytokines. The model identified seven components, two of which had contributions from all blocks (globally joint structure) and five that had contributions from two to five blocks (locally joint structure). Components 1 and 2 were the most informative, identifying differences between healthy controls and asthmatics and a disease–sex interaction, respectively. The interactions between features selected by MB-VIOP were visualized using chord plots, yielding putative novel insights into asthma disease pathogenesis, the effects of asthma treatment, and biological roles of uncharacterized genes. For example, the gene ATP6 V1G1, which has been implicated in osteoporosis, correlated with metabolites that are dysregulated by inhaled corticoid steroids (ICS), providing insight into the mechanisms underlying bone density loss in asthma patients taking ICS. These results show the potential for OnPLS, combined with MB-VIOP variable selection and interaction visualization techniques, to generate hypotheses from multiomics studies and inform biology. |
| first_indexed | 2024-03-07T02:26:08Z |
| format | Journal article |
| id | oxford-uuid:a5adc0ec-ee3b-4d98-8031-b0658c2e9c46 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T02:26:08Z |
| publishDate | 2018 |
| publisher | American Chemical Society |
| record_format | dspace |
| spelling | oxford-uuid:a5adc0ec-ee3b-4d98-8031-b0658c2e9c462022-03-27T02:42:00ZOnPLS-based multi-block data integration: a multivariate approach to interrogating biological interactions in asthmaJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:a5adc0ec-ee3b-4d98-8031-b0658c2e9c46EnglishSymplectic Elements at OxfordAmerican Chemical Society2018Reinke, SNGalindo-Prieto, BSkotare, TBroadhurst, DISinghania, AHorowitz, DDjukanovic, RHinks, TSCGeladi, PTrygg, JWheelock, CEIntegration of multiomics data remains a key challenge in fulfilling the potential of comprehensive systems biology. Multiple-block orthogonal projections to latent structures (OnPLS) is a projection method that simultaneously models multiple data matrices, reducing feature space without relying on a priori biological knowledge. In order to improve the interpretability of OnPLS models, the associated multi-block variable influence on orthogonal projections (MB-VIOP) method is used to identify variables with the highest contribution to the model. This study combined OnPLS and MB-VIOP with interactive visualization methods to interrogate an exemplar multiomics study, using a subset of 22 individuals from an asthma cohort. Joint data structure in six data blocks was assessed: transcriptomics; metabolomics; targeted assays for sphingolipids, oxylipins, and fatty acids; and a clinical block including lung function, immune cell differentials, and cytokines. The model identified seven components, two of which had contributions from all blocks (globally joint structure) and five that had contributions from two to five blocks (locally joint structure). Components 1 and 2 were the most informative, identifying differences between healthy controls and asthmatics and a disease–sex interaction, respectively. The interactions between features selected by MB-VIOP were visualized using chord plots, yielding putative novel insights into asthma disease pathogenesis, the effects of asthma treatment, and biological roles of uncharacterized genes. For example, the gene ATP6 V1G1, which has been implicated in osteoporosis, correlated with metabolites that are dysregulated by inhaled corticoid steroids (ICS), providing insight into the mechanisms underlying bone density loss in asthma patients taking ICS. These results show the potential for OnPLS, combined with MB-VIOP variable selection and interaction visualization techniques, to generate hypotheses from multiomics studies and inform biology. |
| spellingShingle | Reinke, SN Galindo-Prieto, B Skotare, T Broadhurst, DI Singhania, A Horowitz, D Djukanovic, R Hinks, TSC Geladi, P Trygg, J Wheelock, CE OnPLS-based multi-block data integration: a multivariate approach to interrogating biological interactions in asthma |
| title | OnPLS-based multi-block data integration: a multivariate approach to interrogating biological interactions in asthma |
| title_full | OnPLS-based multi-block data integration: a multivariate approach to interrogating biological interactions in asthma |
| title_fullStr | OnPLS-based multi-block data integration: a multivariate approach to interrogating biological interactions in asthma |
| title_full_unstemmed | OnPLS-based multi-block data integration: a multivariate approach to interrogating biological interactions in asthma |
| title_short | OnPLS-based multi-block data integration: a multivariate approach to interrogating biological interactions in asthma |
| title_sort | onpls based multi block data integration a multivariate approach to interrogating biological interactions in asthma |
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