Cargando…

PathwayMultiomics: An R Package for Efficient Integrative Analysis of Multi-Omics Datasets With Matched or Un-matched Samples

Recent advances in technology have made multi-omics datasets increasingly available to researchers. To leverage the wealth of information in multi-omics data, a number of integrative analysis strategies have been proposed recently. However, effectively extracting biological insights from these large...

Descripción completa

Detalles Bibliográficos
Autores principales: Odom, Gabriel J., Colaprico, Antonio, Silva, Tiago C., Chen, X. Steven, Wang, Lily
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8729182/
https://www.ncbi.nlm.nih.gov/pubmed/35003218
http://dx.doi.org/10.3389/fgene.2021.783713
_version_ 1784626884640768000
author Odom, Gabriel J.
Colaprico, Antonio
Silva, Tiago C.
Chen, X. Steven
Wang, Lily
author_facet Odom, Gabriel J.
Colaprico, Antonio
Silva, Tiago C.
Chen, X. Steven
Wang, Lily
author_sort Odom, Gabriel J.
collection PubMed
description Recent advances in technology have made multi-omics datasets increasingly available to researchers. To leverage the wealth of information in multi-omics data, a number of integrative analysis strategies have been proposed recently. However, effectively extracting biological insights from these large, complex datasets remains challenging. In particular, matched samples with multiple types of omics data measured on each sample are often required for multi-omics analysis tools, which can significantly reduce the sample size. Another challenge is that analysis techniques such as dimension reductions, which extract association signals in high dimensional datasets by estimating a few variables that explain most of the variations in the samples, are typically applied to whole-genome data, which can be computationally demanding. Here we present pathwayMultiomics, a pathway-based approach for integrative analysis of multi-omics data with categorical, continuous, or survival outcome variables. The input of pathwayMultiomics is pathway p-values for individual omics data types, which are then integrated using a novel statistic, the MiniMax statistic, to prioritize pathways dysregulated in multiple types of omics datasets. Importantly, pathwayMultiomics is computationally efficient and does not require matched samples in multi-omics data. We performed a comprehensive simulation study to show that pathwayMultiomics significantly outperformed currently available multi-omics tools with improved power and well-controlled false-positive rates. In addition, we also analyzed real multi-omics datasets to show that pathwayMultiomics was able to recover known biology by nominating biologically meaningful pathways in complex diseases such as Alzheimer’s disease.
format Online
Article
Text
id pubmed-8729182
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher Frontiers Media S.A.
record_format MEDLINE/PubMed
spelling pubmed-87291822022-01-06 PathwayMultiomics: An R Package for Efficient Integrative Analysis of Multi-Omics Datasets With Matched or Un-matched Samples Odom, Gabriel J. Colaprico, Antonio Silva, Tiago C. Chen, X. Steven Wang, Lily Front Genet Genetics Recent advances in technology have made multi-omics datasets increasingly available to researchers. To leverage the wealth of information in multi-omics data, a number of integrative analysis strategies have been proposed recently. However, effectively extracting biological insights from these large, complex datasets remains challenging. In particular, matched samples with multiple types of omics data measured on each sample are often required for multi-omics analysis tools, which can significantly reduce the sample size. Another challenge is that analysis techniques such as dimension reductions, which extract association signals in high dimensional datasets by estimating a few variables that explain most of the variations in the samples, are typically applied to whole-genome data, which can be computationally demanding. Here we present pathwayMultiomics, a pathway-based approach for integrative analysis of multi-omics data with categorical, continuous, or survival outcome variables. The input of pathwayMultiomics is pathway p-values for individual omics data types, which are then integrated using a novel statistic, the MiniMax statistic, to prioritize pathways dysregulated in multiple types of omics datasets. Importantly, pathwayMultiomics is computationally efficient and does not require matched samples in multi-omics data. We performed a comprehensive simulation study to show that pathwayMultiomics significantly outperformed currently available multi-omics tools with improved power and well-controlled false-positive rates. In addition, we also analyzed real multi-omics datasets to show that pathwayMultiomics was able to recover known biology by nominating biologically meaningful pathways in complex diseases such as Alzheimer’s disease. Frontiers Media S.A. 2021-12-22 /pmc/articles/PMC8729182/ /pubmed/35003218 http://dx.doi.org/10.3389/fgene.2021.783713 Text en Copyright © 2021 Odom, Colaprico, Silva, Chen and Wang. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Odom, Gabriel J.
Colaprico, Antonio
Silva, Tiago C.
Chen, X. Steven
Wang, Lily
PathwayMultiomics: An R Package for Efficient Integrative Analysis of Multi-Omics Datasets With Matched or Un-matched Samples
title PathwayMultiomics: An R Package for Efficient Integrative Analysis of Multi-Omics Datasets With Matched or Un-matched Samples
title_full PathwayMultiomics: An R Package for Efficient Integrative Analysis of Multi-Omics Datasets With Matched or Un-matched Samples
title_fullStr PathwayMultiomics: An R Package for Efficient Integrative Analysis of Multi-Omics Datasets With Matched or Un-matched Samples
title_full_unstemmed PathwayMultiomics: An R Package for Efficient Integrative Analysis of Multi-Omics Datasets With Matched or Un-matched Samples
title_short PathwayMultiomics: An R Package for Efficient Integrative Analysis of Multi-Omics Datasets With Matched or Un-matched Samples
title_sort pathwaymultiomics: an r package for efficient integrative analysis of multi-omics datasets with matched or un-matched samples
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8729182/
https://www.ncbi.nlm.nih.gov/pubmed/35003218
http://dx.doi.org/10.3389/fgene.2021.783713
work_keys_str_mv AT odomgabrielj pathwaymultiomicsanrpackageforefficientintegrativeanalysisofmultiomicsdatasetswithmatchedorunmatchedsamples
AT colapricoantonio pathwaymultiomicsanrpackageforefficientintegrativeanalysisofmultiomicsdatasetswithmatchedorunmatchedsamples
AT silvatiagoc pathwaymultiomicsanrpackageforefficientintegrativeanalysisofmultiomicsdatasetswithmatchedorunmatchedsamples
AT chenxsteven pathwaymultiomicsanrpackageforefficientintegrativeanalysisofmultiomicsdatasetswithmatchedorunmatchedsamples
AT wanglily pathwaymultiomicsanrpackageforefficientintegrativeanalysisofmultiomicsdatasetswithmatchedorunmatchedsamples