Reconstructing evolving signalling networks by hidden Markov nested effects models

DOI10.1214/13-AOAS696zbMATH Open1454.62250arXiv1405.0849OpenAlexW3098183178WikidataQ57713319 ScholiaQ57713319MaRDI QIDQ2453686FDOQ2453686

Authors: Xin Wang, Ke Yuan, Christoph Hellmayr, Florian Markowetz, Wei Liu 

Publication date: 10 June 2014

Published in: The Annals of Applied Statistics (Search for Journal in Brave)

Abstract: Inferring time-varying networks is important to understand the development and evolution of interactions over time. However, the vast majority of currently used models assume direct measurements of node states, which are often difficult to obtain, especially in fields like cell biology, where perturbation experiments often only provide indirect information of network structure. Here we propose hidden Markov nested effects models (HM-NEMs) to model the evolving network by a Markov chain on a state space of signalling networks, which are derived from nested effects models (NEMs) of indirect perturbation data. To infer the hidden network evolution and unknown parameter, a Gibbs sampler is developed, in which sampling network structure is facilitated by a novel structural Metropolis--Hastings algorithm. We demonstrate the potential of HM-NEMs by simulations on synthetic time-series perturbation data. We also show the applicability of HM-NEMs in two real biological case studies, in one capturing dynamic crosstalk during the progression of neutrophil polarisation, and in the other inferring an evolving network underlying early differentiation of mouse embryonic stem cells.

Full work available at URL: https://arxiv.org/abs/1405.0849

Recommendations

• Nested effects models for learning signaling networks from perturbation data
• Estimating time-varying networks
• Structure learning in nested effects models
• A non-homogeneous dynamic Bayesian network with a hidden Markov model dependency structure among the temporal data points
• A temporal hidden Markov regression model for the analysis of gene regulatory networks

zbMATH Keywords

MCMCdynamicsignalling networkshidden Markovgene pertubationnested effects models

Mathematics Subject Classification ID

Computational methods for problems pertaining to statistics (62-08) Markov processes: estimation; hidden Markov models (62M05) Applications of statistics to biology and medical sciences; meta analysis (62P10)

Cites Work

• Inference from iterative simulation using multiple sequences
• Being Bayesian about network structure. A Bayesian approach to structure discovery in Bayesian networks
• Bayesian Graphical Models for Discrete Data
• Discrete temporal models of social networks
• Title not available (Why is that?)
• Structure learning in nested effects models

Cited In (5)

• Detecting structural changes in longitudinal network data
• Refining cellular pathway models using an ensemble of heterogeneous data sources
• Nested effects models for learning signaling networks from perturbation data
• A motif building process for simulating random networks
• Structure learning in nested effects models

Uses Software

• RedeR

This page was built for publication: Reconstructing evolving signalling networks by hidden Markov nested effects models

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q2453686)