Refining cellular pathway models using an ensemble of heterogeneous data sources

DOI10.1214/16-AOAS915MaRDI QIDQ1620980zbMATH OpenOpenAlexFDO

Authors Alexander M. Franks, Florian Markowetz, E. M. Airoldi

Publication date 15 November 2018

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

Full work available at URL https://arxiv.org/abs/1406.5799, https://projecteuclid.org/euclid.aoas/1536652958

zbMATH Keywords

Bayesian inferencemulti-level modelingregulation and signaling dynamicsstatistical network analysis

Mathematics Subject Classification ID

Bayesian inference (62F15) Applications of statistics to biology and medical sciences; meta analysis (62P10)

Abstract: Building better models of cellular pathways is one of the major challenges of systems biology and functional genomics. There is a need for methods to build on established expert knowledge and reconcile it with results of high-throughput studies. Moreover, the available data sources are heterogeneous and need to be combined in a way specific for the part of the pathway in which they are most informative. Here, we present a compartment specific strategy to integrate edge, node and path data for the refinement of a network hypothesis. Specifically, we use a local-move Gibbs sampler for refining pathway hypotheses from a compendium of heterogeneous data sources, including novel methodology for integrating protein attributes. We demonstrate the utility of this approach in a case study of the pheromone response MAPK pathway in the yeast S. cerevisiae.

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Cites work

• A weakly informative default prior distribution for logistic and other regression models
• Reconstructing evolving signalling networks by hidden Markov nested effects models
• Reconstructing Gene Regulatory Networks with Bayesian Networks by Combining Expression Data with Multiple Sources of Prior Knowledge
• Research in Computational Molecular Biology
• Structure learning in nested effects models

Cited in

(1)

• From genome-scale data to models of infectious disease: a Bayesian network-based strategy to drive model development

Describes a project that uses

Uses Software

• Pfam
• Bioconductor
• SPINE
• R
• KEGG
• BioGRID

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