Identification of Biologically Essential Nodes via Determinative Power in Logical Models of Cellular Processes

Frontiers in Physiology
Trevor PentzienMihaela Teodora Matache

Abstract

A variety of biological networks can be modeled as logical or Boolean networks. However, a simplification of the reality to binary states of the nodes does not ease the difficulty of analyzing the dynamics of large, complex networks, such as signal transduction networks, due to the exponential dependence of the state space on the number of nodes. This paper considers a recently introduced method for finding a fairly small subnetwork, representing a collection of nodes that determine the states of most other nodes with a reasonable level of entropy. The subnetwork contains the most determinative nodes that yield the highest information gain. One of the goals of this paper is to propose an algorithm for finding a suitable subnetwork size. The information gain is quantified by the so-called determinative power of the nodes, which is obtained via the mutual information, a concept originating in information theory. We find the most determinative nodes for 36 network models available in the online database Cell Collective (http://cellcollective.org). We provide statistical information that indicates a weak correlation between the subnetwork size and other variables, such as network size, or maximum and average determinative power of ...Continue Reading

References

Jan 22, 2002·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Sven Bilke, Fredrik Sjunnesson
Mar 14, 2003·Physical Review Letters·J E S Socolar, S A Kauffman
Aug 25, 2004·Physical Review Letters·Ilya Shmulevich, Stuart A Kauffman
Apr 6, 2005·Trends in Pharmacological Sciences·Péter CsermelySándor Pongor
Aug 13, 2005·FEBS Letters·Maria Concetta PalumboLorenzo Farina
Dec 31, 2005·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Viktor KaufmanBarbara Drossel
Dec 31, 2005·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Konstantin Klemm, Stefan Bornholdt
May 12, 2007·FEBS Letters·Maria Concetta PalumboLorenzo Farina
May 16, 2007·Physical Review Letters·Peter Krawitz, Ilya Shmulevich
Aug 29, 2007·PLoS Computational Biology·Julio Saez-RodriguezBurkhart Schraven
Oct 13, 2007·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Peter Krawitz, Ilya Shmulevich
Feb 6, 2008·Proceedings of the National Academy of Sciences of the United States of America·Tomás HelikarJim A Rogers
Mar 21, 2008·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Andre S RibeiroJoshua E S Socolar
Nov 26, 2008·BMC Systems Biology·Gwenael Kervizic, Laurent Corcos
Jan 10, 2009·Nature Protocols·Da Wei HuangRichard A Lempicki
Feb 3, 2009·Journal of Theoretical Biology·D J Irons
May 12, 2009·Bio Systems·A NaldiC Chaouiya
May 11, 2010·Cold Spring Harbor Perspectives in Biology·Haopeng WangArthur Weiss
Aug 7, 2010·Database : the Journal of Biological Databases and Curation·Marilyn SafranDoron Lancet
Sep 13, 2011·Journal of Theoretical Biology·Alan Veliz-Cuba
Nov 15, 2011·Nucleic Acids Research·Wei-Hua ChenPeer Bork
Jan 4, 2012·Bio Systems·Naomi Kochi, Mihaela Teodora Matache
Jul 20, 2012·Science Signaling·Michifumi YamashitaGanes C Sen
Aug 9, 2012·BMC Systems Biology·Tomáš HelikarJim A Rogers
Oct 11, 2012·PloS One·Robert G Todd, Tomáš Helikar
Nov 21, 2012·BMC Genomics·Sriram SridharanJijayanagaram Venkatraj
Apr 4, 2013·Clinical Pharmacology and Therapeutics·T HelikarJ A Rogers
May 7, 2013·EURASIP Journal on Bioinformatics & Systems Biology·Reinhard HeckelMartin Bossert
Oct 2, 2014·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Réka Albert, Juilee Thakar
Feb 13, 2015·Frontiers in Bioengineering and Biotechnology·Wassim Abou-JaoudéDenis Thieffry
Mar 22, 2015·Current Opinion in Structural Biology·Luisa Di Paola, Alessandro Giuliani
Feb 24, 2016·Frontiers in Bioengineering and Biotechnology·Bhanwar Lal PuniyaTomáš Helikar
Jun 16, 2016·Frontiers in Genetics·Wassim Abou-JaoudéClaudine Chaouiya
Jul 16, 2016·Bulletin of Mathematical Biology·Mihaela T Matache, Valentin Matache
Nov 5, 2016·Biochimica Et Biophysica Acta·Maureen Redza-Dutordoir, Diana A Averill-Bates
Dec 28, 2016·PLoS Biology·Mitra MojtahediSui Huang
Jan 1, 2013·SIAM Journal on Applied Dynamical Systems·Assieh SaadatpourTimothy C Reluga

❮ Previous
Next ❯

Citations

Aug 28, 2020·Frontiers in Physiology·Barbara NiederdorferÅsmund Flobak
May 14, 2021·Bioinformatics·Felix M WeidnerHans A Kestler

❮ Previous
Next ❯

Software Mentioned

GINsim
CRISPER
Discovery Collective
Matlab
Cell Collective
DAVID

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.