تقرير
PathIntegrate: Multivariate modelling approaches for pathway-based multi-omics data integration.
| العنوان: | PathIntegrate: Multivariate modelling approaches for pathway-based multi-omics data integration. |
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| المؤلفون: | Wieder, Cecilia, Cooke, Juliette, Frainay, Clement, Poupin, Nathalie, Bowler, Russell, Jourdan, Fabien, Kechris, Katerina J, Lai, Rachel Pj, Ebbels, Timothy |
| المصدر: | bioRxiv |
| بيانات النشر: | PubMed Central |
| سنة النشر: | 2024 |
| المجموعة: | PubMed Central (PMC) |
| الوصف: | As terabytes of multi-omics data are being generated, there is an ever-increasing need for methods facilitating the integration and interpretation of such data. Current multi-omics integration methods typically output lists, clusters, or subnetworks of molecules related to an outcome. Even with expert domain knowledge, discerning the biological processes involved is a time-consuming activity. Here we propose PathIntegrate, a method for integrating multi-omics datasets based on pathways, designed to exploit knowledge of biological systems and thus provide interpretable models for such studies. PathIntegrate employs single-sample pathway analysis to transform multi-omics datasets from the molecular to the pathway-level, and applies a predictive single-view or multi-view model to integrate the data. Model outputs include multi-omics pathways ranked by their contribution to the outcome prediction, the contribution of each omics layer, and the importance of each molecule in a pathway. Using semi-synthetic data we demonstrate the benefit of grouping molecules into pathways to detect signals in low signal-to-noise scenarios, as well as the ability of PathIntegrate to precisely identify important pathways at low effect sizes. Finally, using COPD and COVID-19 data we showcase how PathIntegrate enables convenient integration and interpretation of complex high-dimensional multi-omics datasets. The PathIntegrate Python package is available at https://github.com/cwieder/PathIntegrateTest. |
| نوع الوثيقة: | report |
| اللغة: | English |
| العلاقة: | https://doi.org/10.1101/2024.01.09.574780Test; https://pubmed.ncbi.nlm.nih.gov/38260498Test; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10802464Test/ |
| DOI: | 10.1101/2024.01.09.574780 |
| الإتاحة: | https://doi.org/10.1101/2024.01.09.574780Test https://pubmed.ncbi.nlm.nih.gov/38260498Test https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10802464Test/ |
| رقم الانضمام: | edsbas.E6E9EB8C |
| قاعدة البيانات: | BASE |
| DOI: | 10.1101/2024.01.09.574780 |
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