research-article

Pathway analysis with signaling hypergraphs

Authors:

T. M. MuraliAuthors Info & Claims

BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics

Pages 249 - 258

https://doi.org/10.1145/2649387.2649450

Published: 20 September 2014 Publication History

Abstract

Signaling pathways play an important role in the cell's response to its environment. Signaling pathways are often represented as directed graphs, which are not adequate for modeling reactions such as complex assembly and dissociation, combinatorial regulation, and protein activation/inactivation. More accurate representations such as directed hypergraphs remain underutilized. In this paper, we present an extension of a directed hypergraph that we call a signaling hypergraph. We formulate a problem that asks what proteins and interactions must be involved in order to stimulate a specific response downstream of a signaling pathway. We relate this problem to computing the shortest acyclic B-hyperpath in a signaling hypergraph --- an NP-hard problem --- and present a mixed integer linear program to solve it. We demonstrate that the shortest hyperpaths computed in signaling hypergraphs are far more informative than shortest paths found in corresponding graph representations. Our results illustrate the potential of signaling hypergraphs as an improved representation of signaling pathways and motivate the development of novel hypergraph algorithms.

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Cited By

Preti GFazzone APetri GDe Francisci Morales G(2024)Higher-Order Null Models as a Lens for Social SystemsPhysical Review X10.1103/PhysRevX.14.03103214:3Online publication date: 20-Aug-2024
https://doi.org/10.1103/PhysRevX.14.031032
Krieger SKececioglu J(2024)Computing Robust Optimal Factories in Metabolic Reaction NetworksResearch in Computational Molecular Biology10.1007/978-1-0716-3989-4_16(253-269)Online publication date: 17-May-2024
https://doi.org/10.1007/978-1-0716-3989-4_16
余娩(2023)Design of Min-Max Disjoint Backward Hy-perpaths Algorithm in Acyclic Backward HypergraphAdvances in Applied Mathematics10.12677/AAM.2023.12205612:02(526-536)Online publication date: 2023
https://doi.org/10.12677/AAM.2023.122056
Show More Cited By

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Pathway analysis with signaling hypergraphs

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cover image ACM Conferences

BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics

September 2014

851 pages

ISBN:9781450328944

DOI:10.1145/2649387

General Chairs:
Pierre Baldi
University of California, Irvine
,
Wei Wang
University of California, Los Angeles

Copyright © 2014 ACM.

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than the author(s) must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected].

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Published: 20 September 2014

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BCB '14: ACM-BCB '14

September 20 - 23, 2014

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Cited By

Preti GFazzone APetri GDe Francisci Morales G(2024)Higher-Order Null Models as a Lens for Social SystemsPhysical Review X10.1103/PhysRevX.14.03103214:3Online publication date: 20-Aug-2024
https://doi.org/10.1103/PhysRevX.14.031032
Krieger SKececioglu J(2024)Computing Robust Optimal Factories in Metabolic Reaction NetworksResearch in Computational Molecular Biology10.1007/978-1-0716-3989-4_16(253-269)Online publication date: 17-May-2024
https://doi.org/10.1007/978-1-0716-3989-4_16
余娩(2023)Design of Min-Max Disjoint Backward Hy-perpaths Algorithm in Acyclic Backward HypergraphAdvances in Applied Mathematics10.12677/AAM.2023.12205612:02(526-536)Online publication date: 2023
https://doi.org/10.12677/AAM.2023.122056
Krieger SKececioglu J(2023)Computing Shortest Hyperpaths for Pathway Inference in Cellular Reaction NetworksResearch in Computational Molecular Biology10.1007/978-3-031-29119-7_10(155-173)Online publication date: 3-Apr-2023
https://doi.org/10.1007/978-3-031-29119-7_10
Krieger SKececioglu J(2022)Heuristic shortest hyperpaths in cell signaling hypergraphsAlgorithms for Molecular Biology10.1186/s13015-022-00217-917:1Online publication date: 26-May-2022
https://doi.org/10.1186/s13015-022-00217-9
Franzese NGroce AMurali TRitz A(2019)Hypergraph-based connectivity measures for signaling pathway topologiesPLOS Computational Biology10.1371/journal.pcbi.100738415:10(e1007384)Online publication date: 25-Oct-2019
https://doi.org/10.1371/journal.pcbi.1007384
Ritz AAvent BMurali T(2017)Pathway Analysis with Signaling HypergraphsIEEE/ACM Transactions on Computational Biology and Bioinformatics10.1109/TCBB.2015.245968114:5(1042-1055)Online publication date: 1-Sep-2017
https://dl.acm.org/doi/10.1109/TCBB.2015.2459681
Potter BFix JRitz A(2016)Modeling Cell Signaling Networks with Prize-Collecting SubhypernetworksProceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics10.1145/2975167.2985655(503-504)Online publication date: 2-Oct-2016
https://dl.acm.org/doi/10.1145/2975167.2985655

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