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Patterns of Subnet Usage Reveal Distinct Scales of Regulation in the Transcriptional Regulatory Network of Escherichia coli
Title
Patterns of Subnet Usage Reveal Distinct Scales of Regulation in the Transcriptional Regulatory Network of Escherichia coli.
Creator
Marr, Carsten, Theis, Fabian J., Liebovitch, Larry S., Hütt, Marc-Thorsten, Babu, M. Madan
Abstract/Description
The set of regulatory interactions between genes, mediated by transcription factors, forms a species’ transcriptional regulatory network (TRN). By comparing this network with measured gene expression data, one can identify functional properties of the TRN and gain general insight into transcriptional control. We define the subnet of a node as the subgraph consisting of all nodes topologically downstream of the node, including itself. Using a large set of microarray expression data of the...
Show moreThe set of regulatory interactions between genes, mediated by transcription factors, forms a species’ transcriptional regulatory network (TRN). By comparing this network with measured gene expression data, one can identify functional properties of the TRN and gain general insight into transcriptional control. We define the subnet of a node as the subgraph consisting of all nodes topologically downstream of the node, including itself. Using a large set of microarray expression data of the bacterium Escherichia coli, we find that the gene expression in different subnets exhibits a structured pattern in response to environmental changes and genotypic mutation. Subnets with fewer changes in their expression pattern have a higher fraction of feed-forward loop motifs and a lower fraction of small RNA targets within them. Our study implies that the TRN consists of several scales of regulatory organization: (1) subnets with more varying gene expression controlled by both transcription factors and post-transcriptional RNA regulation and (2) subnets with less varying gene expression having more feed-forward loops and less post-transcriptional RNA regulation.
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Date Issued
2010-07-01
PURL
http://purl.flvc.org/fau/fd/FAUIR000033
Format
Citation
The shape of the eye: why the eye is round
Title
The shape of the eye: why the eye is round.
Creator
Liebovitch, Larry S.
Date Issued
2005
PURL
http://purl.flvc.org/fau/165914
Subject Headings
Eye, Eye--Anatomy, Eye--Physiology
Format
Document (PDF)
Why Nonlinear Biomedical Physics?
Title
Why Nonlinear Biomedical Physics?.
Creator
Czernicki, Zbigniew, Klonowski, Wlodzimierz, Liebovitch, Larry S.
Date Issued
2007-07-05
PURL
http://purl.flvc.org/fcla/dt/3327084
Subject Headings
Biophysics, Medical physics, Nonlinear science, Biomedical engineering
Format
Document (PDF)
Two lessons from fractals and chaos
Title
Two lessons from fractals and chaos.
Creator
Liebovitch, Larry S., Scheurle, Daniela
Date Issued
2000
PURL
http://purl.flvc.org/fau/165936
Subject Headings
Fractals, Nonlinear systems, Mathematical models, Chaos, Chaotic behavior in systems, Biomathematics
Format
Document (PDF)
What is self organization?
Title
What is self organization?.
Creator
Liebovitch, Larry S.
Date Issued
2006-04 - 2006-08
PURL
http://purl.flvc.org/fau/165910
Subject Headings
Biomathematics, Biocomplexity, Self-Organizing systems, Cellular automata--mathematical models, Fractals, Molecules--Mathematical models
Format
Document (PDF)
Introduction to fractals
Title
Introduction to fractals.
Creator
Liebovitch, Larry S., Shehadeh, Lina A.
PURL
http://purl.flvc.org/fau/165810
Subject Headings
Fractals, Chaotic behavior in systems, Nonlinear systems--Mathematical models, Ion channels, Psychology
Format
Document (PDF)
Lévy flights in Dobe Ju/’hoansi foraging patterns
Title
Lévy flights in Dobe Ju/’hoansi foraging patterns.
Creator
Liebovitch, Larry S., Brown, Clifford T., Glendon, Rachel
Date Issued
2007-02-01
PURL
http://purl.flvc.org/fau/165800
Subject Headings
Hunting and gathering societies--statistical methods, Khoisan (African people), Forage, Human Migration Patterns, Human ecology--Africa, Human settlements--Mathematical models, Search theory
Format
Document (PDF)
Developing combinatorial multi-component therapies (CMCT) of drugs that are more specific and have fewer side effects than traditional one drug therapies
Title
Developing combinatorial multi-component therapies (CMCT) of drugs that are more specific and have fewer side effects than traditional one drug therapies.
Creator
Liebovitch, Larry S., Tsinoremas, Nicholas, Pandya, Abhijit S.
Date Issued
2007-08-30
PURL
http://purl.flvc.org/fau/165790
Subject Headings
Drug Therapy, Biomathematics, Combinatorial dynamics, Drugs--Research, Medicine-Mathematics, Biophysics--Research, Nonlinear systems
Format
Document (PDF)
The broken past: fractals in archaeology
Title
The broken past: fractals in archaeology.
Creator
Liebovitch, Larry S., Brown, Clifford T., Witschey, Walter R. T.
Date Issued
2005-03-01
PURL
http://purl.flvc.org/fau/165780
Subject Headings
Fractals, Nonlinear Systems, Chaos, Archaeology--Mathematical models
Format
Document (PDF)
Self-organizing dynamics of coupled map systems
Title
Self-organizing dynamics of coupled map systems.
Creator
Liebovitch, Larry S., Zochowski, Michal
Date Issued
1999-03
PURL
http://purl.flvc.org/fau/165481
Subject Headings
Dynamics--Mathematical models, Chaotic behavior in systems, Self-organizing maps, Self-organizing systems-Mathematical models
Format
Document (PDF)
Information flow dynamics and timing patterns in the arrival of email viruses
Title
Information flow dynamics and timing patterns in the arrival of email viruses.
Creator
Liebovitch, Larry S., Schwartz, Ira B.
Date Issued
2003-07-03
PURL
http://purl.flvc.org/fau/165479
Subject Headings
Information, Computer viruses, Internet, Electronic data processing, Dynamics--Data processing
Format
Document (PDF)
Fractal ion-channel behavior generates fractal firing patterns in neuronal models
Title
Fractal ion-channel behavior generates fractal firing patterns in neuronal models.
Creator
Liebovitch, Larry S., Lowen, Steven B., White, John A.
Date Issued
1999-05
PURL
http://purl.flvc.org/fau/165477
Subject Headings
Biophysics--Research, Fractals, Neural networks (Neurobiology)--Mathematical models, Neurons--Mathematical models, Markov processes--Mathematical models, Ion channels--Mathematical models
Format
Document (PDF)
Dynamics of two-actor cooperation–competition conflict models
Title
Dynamics of two-actor cooperation–competition conflict models.
Creator
Liebovitch, Larry S., Naudot, Vincent, Vallacher, Robin R., Nowak, Andrzej, Bui-Wrzosinska, Lan, Coleman, Peter T.
Date Issued
2008-11-01
PURL
http://purl.flvc.org/fau/165475
Subject Headings
Nonlinear theories, Social systems--Mathematical models, Conflict management, Cooperativeness, Differential equations, Competition, Dynamics--Mathematical models
Format
Document (PDF)
Nonlinear properties of cardiac rhythm abnormalities
Title
Nonlinear properties of cardiac rhythm abnormalities.
Creator
Liebovitch, Larry S., Todorov, Angelo T., Zochowski, Michal, Scheurle, Daniela, Colgin, Laura, Wood, Mark A., Ellenbogen, Kenneth A., Herre, John M., Bernstein, Robert C.
Date Issued
1999-03
PURL
http://purl.flvc.org/fau/165473
Subject Headings
Biophysics--Research, Medicine-Mathematics, Arrythmia--therapy, Fractals, Nonlinear systems, Probabilities-Mathematical Models
Format
Document (PDF)
Relationships between the global structure of genetic networks and mRNA levels measured by cDNA microarrays
Title
Relationships between the global structure of genetic networks and mRNA levels measured by cDNA microarrays.
Creator
Liebovitch, Larry S., Shehadeh, Lina A., Jirsa, Viktor K.
Date Issued
2006-05-16
PURL
http://purl.flvc.org/fau/165446
Subject Headings
DNA microarrays, DNA--genetics, Gene Expression Regulation, DNA- protein interactions, Genetic regulation, Messenger RNA--Analysis
Format
Document (PDF)
Is there an error correcting code in the base sequence in DNA?
Title
Is there an error correcting code in the base sequence in DNA?.
Creator
Liebovitch, Larry S., Levine, Leo, Tao, Yi, Todorov, Angelo T.
Date Issued
1996-09
PURL
http://purl.flvc.org/fau/165441
Subject Headings
Biophysics--Research, DNA, Genetics, DNA Repair--genetics, DNA--Analysis--Mathematical models, Genetic code
Format
Document (PDF)
Hurst analysis applied to the study of single calcium-activated potassium channel kinetics
Title
Hurst analysis applied to the study of single calcium-activated potassium channel kinetics.
Creator
Liebovitch, Larry S., Figueiroa, Josed N., Nogueira, Romildo A., Varanda, Wamberto A.
Date Issued
2000-10-07
PURL
http://purl.flvc.org/FAU/165249
Subject Headings
Ion channels-Mathematical models, Memory, Chemical kinetics, Calcium channels, Fractals, Markov processes, Leydig cells, Molecular biology--Statistical methods
Format
Document (PDF)
Fractal methods to analyze ion channel kinetics
Title
Fractal methods to analyze ion channel kinetics.
Creator
Liebovitch, Larry S., Scheurle, Daniela, Rusek, Marian, Zochowskis, Michal
Date Issued
2001-08
PURL
http://purl.flvc.org/FAU/165246
Subject Headings
Fractals, Ion Channels-Mathematical models, Ion flow dynamics, Biomathematics, Chaotic behavior in systems
Format
Document (PDF)
Dynamical response of multi-patch, flux-based models to the input of infected people: epidemic response to initiated events
Title
Dynamical response of multi-patch, flux-based models to the input of infected people: epidemic response to initiated events.
Creator
Liebovitch, Larry S., Schwartz, Ira B., Rho, Young-Ah
Date Issued
2008-07-21
PURL
http://purl.flvc.org/FAU/165229
Subject Headings
Communicable diseases--Epidemiology--Mathematical models, Epidemiologic Methods, Differential equations, Dynamics--Mathematical models, Spatial systems--Mathematical models, Population dynamics, Emerging infectious diseases
Format
Document (PDF)
Migration induced epidemics: dynamics of flux-based multipatch models
Title
Migration induced epidemics: dynamics of flux-based multipatch models.
Creator
Liebovitch, Larry S., Schwartz, Ira B.
Date Issued
2004
PURL
http://purl.flvc.org/FAU/165227
Subject Headings
Communicable diseases--Epidemiology--Mathematical models, Emerging infectious diseases, Epidemiologic Methods, Epidemiology, Biomathematics, Medicine-Mathematics, Dynamics-Mathematical models
Format
Document (PDF)