A Combined PLS and Negative Binomial Regression Model for Inferring Association Networks from Next-generation Sequencing Count Data
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A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
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Date
2018-05-01
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en
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14
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IEEE/ACM Transactions on Computational Biology and Bioinformatics
Abstract
A major challenge of genomics data is to detect interactions displaying functional associations from large-scale observations. In this study, a new cPLS-algorithm combining partial least squares approach with negative binomial regression is suggested to reconstruct a genomic association network for high-dimensional next-generation sequencing count data. The suggested approach is applicable to the raw counts data, without requiring any further pre-processing steps. In the settings investigated, the cPLS-algorithm outperformed the two widely used comparative methods, graphical lasso and weighted correlation network analysis. In addition, cPLS is able to estimate the full network for thousands of genes without major computational load. Finally, we demonstrate that cPLS is capable of finding biologically meaningful associations by analysing an example data set from a previously published study to examine the molecular anatomy of the craniofacial development.Description
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association networks, network reconstruction, negative binomial regression, next-generation sequencing, partial least-squares regression
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Citation
Pesonen, M, Nevalainen, J, Potter, S, Datta, S & Datta, S 2018, ' A Combined PLS and Negative Binomial Regression Model for Inferring Association Networks from Next-generation Sequencing Count Data ', IEEE-ACM Transactions on Computational Biology and Bioinformatics, vol. 15, no. 3, pp. 760-773 . https://doi.org/10.1109/TCBB.2017.2665495