Comprehensive evaluation of methods for differential expression analysis of metatranscriptomics data

H, Cho; C, Liu; Bm, Lin; Tang, Baihua; Roach, Jeff; A, de Ribeiro; Mi, Love; Divaris, Kimon; Wu, Di

doi:10.1101/2021.07.14.452374

Cited by 2 publications

(2 citation statements)

References 98 publications

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“…The focus of the work reported in this paper is metagenomics data at the species level, but our new method can be applied to metatranscriptomics (i.e., RNAseq), as well as other levels of data, including gene-family or genes, because all data types are similarly characterized by excess zeros and overdispersion [20].…”

Section: Existing Correlation Calculation Methods For Network/pathway...mentioning

confidence: 99%

BZINB model-based pathway analysis and module identification facilitates integration of microbiome and metabolome data

Lin¹,

Cho²,

Liu³

et al. 2023

Preprint

Self Cite

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Integration of multi-omics data is a challenging but necessary step to advance our understanding of the biology underlying human health and disease processes. To date, investigations seeking to integrate multi-omics (e.g., microbiome and metabolome) employ simple correlation-based network analyses; however, these methods are not always well-suited for microbiome analyses because they do not accommodate the excess zeros typically present in these data. In this paper, we introduce a bivariate zero-inflated negative binomial (BZINB) model-based network and module analysis method that addresses this limitation and improves microbiome-metabolome correlation-based model fitting by accommodating excess zeros. We use real and simulated data based on a multi-omics study of childhood oral health (ZOE 2.0; investigating early childhood dental disease, ECC) and find that the accuracy of the BZINB model-based correlation method is superior compared to Spearman's rank and Pearson correlations in terms of approximating the underlying relationships between microbial taxa and metabolites. The new method, BZINB-iMMPath facilitates the construction of metabolite-species and species-species correlation networks using BZINB and identifies modules of (i.e., correlated) species by combining BZINB and similarity-based clustering. Perturbations in correlation networks and modules can be efficiently tested between groups (i.e., healthy and diseased study participants). Upon application of the new method in the ZOE 2.0 study microbiome-metabolome data, we identify that several biologically-relevant correlations of ECC-associated microbial taxa with carbohydrate metabolites differ between healthy and dental caries-affected participants. In sum, we find that the BZINB model is a useful alternative to Spearman or Pearson correlations for estimating the underlying correlation of zero-inflated bivariate count data and thus is suitable for integrative analyses of multi-omics data such as those encountered in microbiome and metabolome studies.

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Section: Existing Correlation Calculation Methods For Network/pathway...mentioning

confidence: 99%

BZINB model-based pathway analysis and module identification facilitates integration of microbiome and metabolome data

Lin¹,

Cho²,

Liu³

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…The focus of the work reported in this paper is metagenomics data at the species level, but our new method can be applied to metatranscriptomics (i.e., RNAseq) as well as other levels of data, including gene family or genes, because all data types are similarly characterized by excess zeros and overdispersion [ 26 ].…”

Section: Methodsmentioning

confidence: 99%

BZINB Model-Based Pathway Analysis and Module Identification Facilitates Integration of Microbiome and Metabolome Data

et al. 2023

Self Cite

View full text Add to dashboard Cite

Integration of multi-omics data is a challenging but necessary step to advance our understanding of the biology underlying human health and disease processes. To date, investigations seeking to integrate multi-omics (e.g., microbiome and metabolome) employ simple correlation-based network analyses; however, these methods are not always well-suited for microbiome analyses because they do not accommodate the excess zeros typically present in these data. In this paper, we introduce a bivariate zero-inflated negative binomial (BZINB) model-based network and module analysis method that addresses this limitation and improves microbiome–metabolome correlation-based model fitting by accommodating excess zeros. We use real and simulated data based on a multi-omics study of childhood oral health (ZOE 2.0; investigating early childhood dental caries, ECC) and find that the accuracy of the BZINB model-based correlation method is superior compared to Spearman’s rank and Pearson correlations in terms of approximating the underlying relationships between microbial taxa and metabolites. The new method, BZINB-iMMPath, facilitates the construction of metabolite–species and species–species correlation networks using BZINB and identifies modules of (i.e., correlated) species by combining BZINB and similarity-based clustering. Perturbations in correlation networks and modules can be efficiently tested between groups (i.e., healthy and diseased study participants). Upon application of the new method in the ZOE 2.0 study microbiome–metabolome data, we identify that several biologically-relevant correlations of ECC-associated microbial taxa with carbohydrate metabolites differ between healthy and dental caries-affected participants. In sum, we find that the BZINB model is a useful alternative to Spearman or Pearson correlations for estimating the underlying correlation of zero-inflated bivariate count data and thus is suitable for integrative analyses of multi-omics data such as those encountered in microbiome and metabolome studies.

show abstract

Comprehensive evaluation of methods for differential expression analysis of metatranscriptomics data

Cited by 2 publications

References 98 publications

BZINB model-based pathway analysis and module identification facilitates integration of microbiome and metabolome data

BZINB model-based pathway analysis and module identification facilitates integration of microbiome and metabolome data

BZINB Model-Based Pathway Analysis and Module Identification Facilitates Integration of Microbiome and Metabolome Data

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