3-way Networks: Application of Hypergraphs for Modelling Increased Complexity in Comparative Genomics
Abstract
In this paper, we present and develop the theory 3-way networks, a type of hypergraph in which each edge models relationships between triplets of objects as opposed to pairs of objects as done by standard network models. We explore approaches of how to prune these 3-way networks, illustrate their utility in comparative genomics and demonstrate how they find relationships which would be missed by standard 2-way network models using a phylogenomic dataset of 211 bacterial genomes.
- Authors:
-
- Stellenbosch Univ., Stellenbosch (South Africa); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
- Stellenbosch Univ., Stellenbosch (South Africa); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1260601
- Alternate Identifier(s):
- OSTI ID: 1265407
- Grant/Contract Number:
- PS02-06ER64304; AC05-00OR22725
- Resource Type:
- Accepted Manuscript
- Journal Name:
- PLoS Computational Biology (Online)
- Additional Journal Information:
- Journal Name: PLoS Computational Biology (Online); Journal Volume: 11; Journal Issue: 3; Journal ID: ISSN 1553-7358
- Publisher:
- Public Library of Science
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 97 MATHEMATICS AND COMPUTING
Citation Formats
Weighill, Deborah A., and Jacobson, Daniel A. 3-way Networks: Application of Hypergraphs for Modelling Increased Complexity in Comparative Genomics. United States: N. p., 2015.
Web. doi:10.1371/journal.pcbi.1004079.
Weighill, Deborah A., & Jacobson, Daniel A. 3-way Networks: Application of Hypergraphs for Modelling Increased Complexity in Comparative Genomics. United States. https://doi.org/10.1371/journal.pcbi.1004079
Weighill, Deborah A., and Jacobson, Daniel A. Fri .
"3-way Networks: Application of Hypergraphs for Modelling Increased Complexity in Comparative Genomics". United States. https://doi.org/10.1371/journal.pcbi.1004079. https://www.osti.gov/servlets/purl/1260601.
@article{osti_1260601,
title = {3-way Networks: Application of Hypergraphs for Modelling Increased Complexity in Comparative Genomics},
author = {Weighill, Deborah A. and Jacobson, Daniel A.},
abstractNote = {In this paper, we present and develop the theory 3-way networks, a type of hypergraph in which each edge models relationships between triplets of objects as opposed to pairs of objects as done by standard network models. We explore approaches of how to prune these 3-way networks, illustrate their utility in comparative genomics and demonstrate how they find relationships which would be missed by standard 2-way network models using a phylogenomic dataset of 211 bacterial genomes.},
doi = {10.1371/journal.pcbi.1004079},
journal = {PLoS Computational Biology (Online)},
number = 3,
volume = 11,
place = {United States},
year = {Fri Mar 27 00:00:00 EDT 2015},
month = {Fri Mar 27 00:00:00 EDT 2015}
}
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Works referenced in this record:
A comparative genomic view of clostridial sporulation and physiology
journal, October 2005
- Paredes, Carlos J.; Alsaker, Keith V.; Papoutsakis, Eleftherios T.
- Nature Reviews Microbiology, Vol. 3, Issue 12
Decomposition of Flux Distributions into Metabolic Pathways
journal, July 2013
- Seref, Onur; Brooks, J. Paul; Fong, Stephen S.
- IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 10, Issue 4
Use of ternary similarities in graph based clustering for protein structural family classification
conference, January 2010
- Santini, Guillaume; Soldano, Henry; Pothier, Joël
- Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology - BCB '10
Whole-Genome-Based Phylogeny and Divergence of the Genus Brucella
journal, February 2009
- Foster, Jeffrey T.; Beckstrom-Sternberg, Stephen M.; Pearson, Talima
- Journal of Bacteriology, Vol. 191, Issue 8
Bayesian evolutionary hypergraph learning for predicting cancer clinical outcomes
journal, June 2014
- Kim, Soo-Jin; Ha, Jung-Woo; Zhang, Byoung-Tak
- Journal of Biomedical Informatics, Vol. 49
Rahnuma: hypergraph-based tool for metabolic pathway prediction and network comparison
journal, April 2009
- Mithani, Aziz; Preston, Gail M.; Hein, Jotun
- Bioinformatics, Vol. 25, Issue 14
An Ordination of the Upland Forest Communities of Southern Wisconsin
journal, February 1957
- Bray, J. Roger; Curtis, J. T.
- Ecological Monographs, Vol. 27, Issue 4
A multiple-site similarity measure
journal, October 2006
- Diserud, Ola H.; Ødegaard, Frode
- Biology Letters, Vol. 3, Issue 1
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
journal, November 2003
- Shannon, P.
- Genome Research, Vol. 13, Issue 11
Basic local alignment search tool
journal, October 1990
- Altschul, Stephen F.; Gish, Warren; Miller, Webb
- Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410
Network biology: understanding the cell's functional organization
journal, February 2004
- Barabási, Albert-László; Oltvai, Zoltán N.
- Nature Reviews Genetics, Vol. 5, Issue 2
Constructing higher-order miRNA-mRNA interaction networks in prostate cancer via hypergraph-based learning
journal, January 2013
- Kim, Soo-Jin; Ha, Jung-Woo; Zhang, Byoung-Tak
- BMC Systems Biology, Vol. 7, Issue 1
MOLECULAR GENETICS OF SPORULATION IN BACILLUS SUBTILIS
journal, December 1996
- Stragier, Patrick; Losick, Richard
- Annual Review of Genetics, Vol. 30, Issue 1
Exploring photosynthesis evolution by comparative analysis of metabolic networks between chloroplasts and photosynthetic bacteria
journal, April 2006
- Wang, Zhuo; Zhu, Xin-Guang; Chen, Yazhu
- BMC Genomics, Vol. 7, Issue 1
An efficient algorithm for large-scale detection of protein families
journal, April 2002
- Enright, A. J.
- Nucleic Acids Research, Vol. 30, Issue 7
The Logic of Inductive Inference
journal, January 1935
- Fisher, R. A.
- Journal of the Royal Statistical Society, Vol. 98, Issue 1
Characterization of a Polysaccharide Deacetylase Gene Homologue (pdaB) on Sporulation of Bacillus subtilis
journal, September 2004
- Fukushima, T.
- Journal of Biochemistry, Vol. 136, Issue 3
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
journal, September 2003
- Li, L.
- Genome Research, Vol. 13, Issue 9
Feature Correlation Hypergraph: Exploiting High-order Potentials for Multimodal Recognition
journal, August 2014
- Zhang, Luming; Gao, Yue; Hong, Chaoqun
- IEEE Transactions on Cybernetics, Vol. 44, Issue 8
Similarity indices, sample size and diversity
journal, September 1981
- Wolda, Henk
- Oecologia, Vol. 50, Issue 3
A comparative genomic view of clostridial sporulation and physiology
journal, October 2005
- Paredes, Carlos J.; Alsaker, Keith V.; Papoutsakis, Eleftherios T.
- Nature Reviews Microbiology, Vol. 3, Issue 12
Comparative transcriptomic analysis reveals conserved programmes underpinning organogenesis and reproduction in land plants
journal, July 2021
- Julca, Irene; Ferrari, Camilla; Flores-Tornero, María
- Nature Plants, Vol. 7, Issue 8
Preterm infants with isolated cerebellar hemorrhage show bilateral cortical alterations at term equivalent age
journal, March 2020
- Dijkshoorn, Aicha B. C.; Turk, Elise; Hortensius, Lisa M.
- Scientific Reports, Vol. 10, Issue 1
An efficient algorithm for large-scale detection of protein families
journal, April 2002
- Enright, A. J.
- Nucleic Acids Research, Vol. 30, Issue 7
NCBI BLAST: a better web interface
journal, May 2008
- Johnson, M.; Zaretskaya, I.; Raytselis, Y.
- Nucleic Acids Research, Vol. 36, Issue Web Server
A multiple-site similarity measure
journal, October 2006
- Diserud, Ola H.; Ødegaard, Frode
- Biology Letters, Vol. 3, Issue 1
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
journal, September 2003
- Li, L.
- Genome Research, Vol. 13, Issue 9
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
journal, November 2003
- Shannon, P.
- Genome Research, Vol. 13, Issue 11
A Polysaccharide Deacetylase Gene (pdaA) Is Required for Germination and for Production of Muramic δ-Lactam Residues in the Spore Cortex of Bacillus subtilis
journal, November 2002
- Fukushima, Tatsuya; Yamamoto, Hiroki; Atrih, Abdelmadjid
- Journal of Bacteriology, Vol. 184, Issue 21
MOLECULAR GENETICS OF SPORULATION IN BACILLUS SUBTILIS
journal, December 1996
- Stragier, Patrick; Losick, Richard
- Annual Review of Genetics, Vol. 30, Issue 1
Exploring photosynthesis evolution by comparative analysis of metabolic networks between chloroplasts and photosynthetic bacteria
journal, April 2006
- Wang, Zhuo; Zhu, Xin-Guang; Chen, Yazhu
- BMC Genomics, Vol. 7, Issue 1
Constructing higher-order miRNA-mRNA interaction networks in prostate cancer via hypergraph-based learning
journal, January 2013
- Kim, Soo-Jin; Ha, Jung-Woo; Zhang, Byoung-Tak
- BMC Systems Biology, Vol. 7, Issue 1
An Ordination of the Upland Forest Communities of Southern Wisconsin
journal, February 1957
- Bray, J. Roger; Curtis, J. T.
- Ecological Monographs, Vol. 27, Issue 4
Works referencing / citing this record:
Fungal-Bacterial Networks in the Populus Rhizobiome Are Impacted by Soil Properties and Host Genotype
journal, March 2019
- Bonito, Gregory; Benucci, Gian Maria Niccolò; Hameed, Khalid
- Frontiers in Microbiology, Vol. 10