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Differential Co-Abundance Network Analyses for Microbiome Data Adjusted for Clinical Covariates Using Jackknife Pseudo-Values

A recent breakthrough in differential network (DN) analysis of microbiome data has been realized with the advent of next-generation sequencing technologies. The DN analysis disentangles the microbial co-abundance among taxa by comparing the network properties between two or more graphs under differe...

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Autores principales: Ahn, Seungjun, Datta, Somnath
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cornell University 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10055480/
https://www.ncbi.nlm.nih.gov/pubmed/36994149
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author Ahn, Seungjun
Datta, Somnath
author_facet Ahn, Seungjun
Datta, Somnath
author_sort Ahn, Seungjun
collection PubMed
description A recent breakthrough in differential network (DN) analysis of microbiome data has been realized with the advent of next-generation sequencing technologies. The DN analysis disentangles the microbial co-abundance among taxa by comparing the network properties between two or more graphs under different biological conditions. However, the existing methods to the DN analysis for microbiome data do not adjust for other clinical differences between subjects. We propose a Statistical Approach via Pseudo-value Information and Estimation for Differential Network Analysis (SOHPIE-DNA) that incorporates additional covariates such as continuous age and categorical BMI. SOHPIE-DNA is a regression technique adopting jackknife pseudo-values that can be implemented readily for the analysis. We demonstrate through simulations that SOHPIE-DNA consistently reaches higher recall and F1-score, while maintaining similar precision and accuracy to existing methods (NetCoMi and MDiNE). Lastly, we apply SOHPIE-DNA on two real datasets from the American Gut Project and the Diet Exchange Study to showcase the utility. The analysis of the Diet Exchange Study is to showcase that SOHPIE-DNA can also be used to incorporate the temporal change of connectivity of taxa with the inclusion of additional covariates. As a result, our method has found taxa that are related to the prevention of intestinal inflammation and severity of fatigue in advanced metastatic cancer patients.
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spelling pubmed-100554802023-03-30 Differential Co-Abundance Network Analyses for Microbiome Data Adjusted for Clinical Covariates Using Jackknife Pseudo-Values Ahn, Seungjun Datta, Somnath ArXiv Article A recent breakthrough in differential network (DN) analysis of microbiome data has been realized with the advent of next-generation sequencing technologies. The DN analysis disentangles the microbial co-abundance among taxa by comparing the network properties between two or more graphs under different biological conditions. However, the existing methods to the DN analysis for microbiome data do not adjust for other clinical differences between subjects. We propose a Statistical Approach via Pseudo-value Information and Estimation for Differential Network Analysis (SOHPIE-DNA) that incorporates additional covariates such as continuous age and categorical BMI. SOHPIE-DNA is a regression technique adopting jackknife pseudo-values that can be implemented readily for the analysis. We demonstrate through simulations that SOHPIE-DNA consistently reaches higher recall and F1-score, while maintaining similar precision and accuracy to existing methods (NetCoMi and MDiNE). Lastly, we apply SOHPIE-DNA on two real datasets from the American Gut Project and the Diet Exchange Study to showcase the utility. The analysis of the Diet Exchange Study is to showcase that SOHPIE-DNA can also be used to incorporate the temporal change of connectivity of taxa with the inclusion of additional covariates. As a result, our method has found taxa that are related to the prevention of intestinal inflammation and severity of fatigue in advanced metastatic cancer patients. Cornell University 2023-03-23 /pmc/articles/PMC10055480/ /pubmed/36994149 Text en https://creativecommons.org/licenses/by/4.0/This work is licensed under a Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/) , which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use.
spellingShingle Article
Ahn, Seungjun
Datta, Somnath
Differential Co-Abundance Network Analyses for Microbiome Data Adjusted for Clinical Covariates Using Jackknife Pseudo-Values
title Differential Co-Abundance Network Analyses for Microbiome Data Adjusted for Clinical Covariates Using Jackknife Pseudo-Values
title_full Differential Co-Abundance Network Analyses for Microbiome Data Adjusted for Clinical Covariates Using Jackknife Pseudo-Values
title_fullStr Differential Co-Abundance Network Analyses for Microbiome Data Adjusted for Clinical Covariates Using Jackknife Pseudo-Values
title_full_unstemmed Differential Co-Abundance Network Analyses for Microbiome Data Adjusted for Clinical Covariates Using Jackknife Pseudo-Values
title_short Differential Co-Abundance Network Analyses for Microbiome Data Adjusted for Clinical Covariates Using Jackknife Pseudo-Values
title_sort differential co-abundance network analyses for microbiome data adjusted for clinical covariates using jackknife pseudo-values
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10055480/
https://www.ncbi.nlm.nih.gov/pubmed/36994149
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