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Network analysis for count data with excess zeros

Title
Network analysis for count data with excess zeros
Authors
Choi H.Gim J.Won S.Kim Y.J.Kwon S.Park C.
Ewha Authors
김유진
Issue Date
2017
Journal Title
BMC Genetics
ISSN
1471-2156JCR Link
Citation
BMC Genetics vol. 18, no. 1
Keywords
Count dataEM algorithmNetworkZero inflation
Publisher
BioMed Central Ltd.
Indexed
SCIE; SCOPUS WOS scopus
Document Type
Article
Abstract
Background: Undirected graphical models or Markov random fields have been a popular class of models for representing conditional dependence relationships between nodes. In particular, Markov networks help us to understand complex interactions between genes in biological processes of a cell. Local Poisson models seem to be promising in modeling positive as well as negative dependencies for count data. Furthermore, when zero counts are more frequent than are expected, excess zeros should be considered in the model. Methods: We present a penalized Poisson graphical model for zero inflated count data and derive an expectation-maximization (EM) algorithm built on coordinate descent. Our method is shown to be effective through simulated and real data analysis. Results: Results from the simulated data indicate that our method outperforms the local Poisson graphical model in the presence of excess zeros. In an application to a RNA sequencing data, we also investigate the gender effect by comparing the estimated networks according to different genders. Our method may help us in identifying biological pathways linked to sex hormone regulation and thus understanding underlying mechanisms of the gender differences. Conclusions: We have presented a penalized version of zero inflated spatial Poisson regression and derive an efficient EM algorithm built on coordinate descent. We discuss possible improvements of our method as well as potential research directions associated with our findings from the RNA sequencing data. © 2017 The Author(s).
DOI
10.1186/s12863-017-0561-z
Appears in Collections:
신산업융합대학 > 식품영양학과 > Journal papers
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