MBMM: Moment Estimating Beta Mixture Model-based Clustering Algorithm for m6A Co-methylation Module Mining

Author(s): Zhaoyang Liu, Hongsheng Yin*, Shutao Chen, Hui Liu, Jia Meng, HongLei Wang, Lin Zhang*

Journal Name: Current Bioinformatics

Volume 16 , Issue 10 , 2021


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Abstract:

Background: m6A methylation is a ubiquitous post-transcriptional modification that exists in mammals. MeRIP-seq technology makes the acquisition of m6A data in the whole transcriptome under different conditions realizable. The specific regulation of the enzyme will present comethylation module on m6A methylation level data. Thus, mining the co-methylation module from which can help to unveil the mechanism of m6A methylation modification and its mechanism in the occurrence and development of complex diseases such as cancer.

Objective: To develop a clustering algorithm that can effectively realize the mining of m6A comethylation module.

Methods: In this study, a novel beta mixture model-based clustering algorithm named MBMM was proposed, which is based on the EM framework and introduces the method of moment estimating in M-step for parameter estimation to tackle the high-dimensional small sample m6A data. Simulation research was employed to evaluate the clustering performance of the proposed algorithm, and by which the co-methylation module mining was done based on real data. Biological significance correlation analysis was employed to explore whether the clustering results are co-methylation modules.

Results and Conclusion: Simulation research demonstrated that MBMM performed out than other clustering algorithms. In real data, seven co-methylation modules were found by MBMM. Six m6Arelated pathways specific analysis showed that six co-methylation modules were enriched in the pathway and were different. Five enzymes substrate-specific analysis revealed that seven comethylation modules expressed varying degrees of enrichment. Gene Ontology enrichment analysis indicated that these modules may be regulated by enzymes while having potential functional specificity.

Keywords: m6A, methylation, co-methylation module, beta mixture model, clustering, data mining.

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Article Details

VOLUME: 16
ISSUE: 10
Year: 2021
Published on: 13 August, 2021
Page: [1244 - 1256]
Pages: 13
DOI: 10.2174/1574893616666210629143411

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