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Title: Hypergraph Models of Biological Networks to Identify Genes Critical to Pathogenic Viral Response

Journal Article · · BMC Bioinformatics
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  1. BATTELLE (PACIFIC NW LAB)
  2. University of Wisconsin-Madison
  3. Washington University In Saint Louis
  4. University of North Carolina
  5. University of North Carolina at Chapel Hill
+ Show Author Affiliations

Motivation: Representing biological networks as graphs is a powerful approach to reveal underlying patterns, signatures, and critical components from high-throughput biomolecular data. However, graphs do not natively capture the multi-way relationships present among genes and proteins in biological systems such as protein complexes, metabolic reactions, and signal transduction pathways. Hypergraphs are generalizations of graphs that naturally model multi-way interactions in data, and we therefore seek to understand how they can more faithfully identify, and potentially predict, complex relationships in genomic expression data sets. Results: We compiled a novel data set of transcriptional host response to pathogenic viral infections and formulated relationships between genes as a hypergraph where hyperedges are differentially expressed genes and vertices represent conditions. We find that hypergraph betweenness centrality is a superior method for identification of genes important to viral response when compared with graph centrality. Our results demonstrate the utility of using hypergraphs to represent complex biological systems, and highlight potentially interesting biological results about host response to highly pathogenic viruses.

Research Organization:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Organization:
USDOE
DOE Contract Number:
AC05-76RL01830
OSTI ID:
1807906
Report Number(s):
PNNL-SA-155930
Journal Information:
BMC Bioinformatics, Vol. 22, Issue 1
Country of Publication:
United States
Language:
English

References (30)

The effect of inhibition of PP1 and TNFα signaling on pathogenesis of SARS coronavirus journal September 2016
The Role of EGFR in Influenza Pathogenicity: Multiple Network-Based Approaches to Identify a Key Regulator of Non-lethal Infections journal September 2019
Heterogeneous networks integration for disease–gene prioritization with node kernels journal January 2020
Correlation network analysis for data integration and biomarker selection journal January 2008
Temporal Proteome and Lipidome Profiles Reveal Hepatitis C Virus-Associated Reprogramming of Hepatocellular Metabolism and Bioenergetics journal January 2010
Impact of Dietary Resistant Starch on the Human Gut Microbiome, Metaproteome, and Metabolome journal October 2017
Unified feature association networks through integration of transcriptomic and proteomic data journal September 2019
Systematic identification of metabolites controlling gene expression in E. coli journal October 2019
Modeling Dynamic Regulatory Processes in Stroke journal October 2012
A model of cyclic transcriptomic behavior in the cyanobacterium Cyanothece sp. ATCC 51142 journal January 2011
Simplicial models of social contagion journal June 2019
Hypergraphs and Cellular Networks journal May 2009
The shape of collaborations journal August 2017
On a hypergraph probabilistic graphical model journal July 2020
Formal structure of periodic system of elements journal April 2019
A hypergraph model for the yeast protein complex network conference January 2004
Properties of metabolic graphs: biological organization or representation artifacts? journal May 2011
Advantages and limitations of current network inference methods journal August 2010
Identification and Validation of Ifit1 as an Important Innate Immune Bottleneck journal June 2012
Pathogenic Influenza Viruses and Coronaviruses Utilize Similar and Contrasting Approaches To Control Interferon-Stimulated Gene Responses journal May 2014
A Network Integration Approach to Predict Conserved Regulators Related to Pathogenicity of Influenza and SARS-CoV Respiratory Viruses journal July 2013
Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles journal January 2007
The Landscape of Human Proteins Interacting with Viruses and Other Pathogens journal January 2008
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles journal September 2005
Identification of critical connectors in the directed reaction-centric graphs of microbial metabolic networks journal June 2019
The ZZ-type zinc finger of ZZZ3 modulates the ATAC complex-mediated histone acetylation and gene activation journal September 2018
Host Regulatory Network Response to Infection with Highly Pathogenic H5N1 Avian Influenza Virus journal August 2011
Hypernetwork science via high-order hypergraph walks journal June 2020
The Importance of Bottlenecks in Protein Networks: Correlation with Gene Essentiality and Expression Dynamics journal January 2007
Bottlenecks and Hubs in Inferred Networks Are Important for Virulence in Salmonella typhimurium journal February 2009

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Related Subjects

systems biology
hypergraph
viral infection
biological networks
SARS
MERS
influenza
West Nile virus
host response
viral pathogenesis