Structural analysis to determine the core of hypoxia response network.

PloS One
Monika Heiner, K Sriram

Abstract

The advent of sophisticated molecular biology techniques allows to deduce the structure of complex biological networks. However, networks tend to be huge and impose computational challenges on traditional mathematical analysis due to their high dimension and lack of reliable kinetic data. To overcome this problem, complex biological networks are decomposed into modules that are assumed to capture essential aspects of the full network's dynamics. The question that begs for an answer is how to identify the core that is representative of a network's dynamics, its function and robustness. One of the powerful methods to probe into the structure of a network is Petri net analysis. Petri nets support network visualization and execution. They are also equipped with sound mathematical and formal reasoning based on which a network can be decomposed into modules. The structural analysis provides insight into the robustness and facilitates the identification of fragile nodes. The application of these techniques to a previously proposed hypoxia control network reveals three functional modules responsible for degrading the hypoxia-inducible factor (HIF). Interestingly, the structural analysis identifies superfluous network parts and suggests...Continue Reading

References

Jun 6, 1995·Proceedings of the National Academy of Sciences of the United States of America·G L WangG L Semenza
Jun 17, 1998·Proceedings of the National Academy of Sciences of the United States of America·P J Goss, J Peccoud
Dec 11, 1999·Nature·L H HartwellA W Murray
Jul 16, 2004·Seminars in Radiation Oncology·Peter Vaupel
Sep 17, 2004·Cell·Jörg StellingJohn Doyle
Nov 3, 2004·Nature Reviews. Genetics·Hiroaki Kitano
May 11, 2005·Nature Reviews. Genetics·Mads KaernJames J Collins
Feb 17, 2006·Journal of Perinatology : Official Journal of the California Perinatal Association·O D Saugstad
Aug 11, 2006·Journal of Cell Science·Amina A Qutub, Aleksander S Popel
Jul 13, 2007·Briefings in Bioinformatics·Claudine Chaouiya
Sep 21, 2007·Molecular Systems Biology·Hiroaki Kitano
Dec 1, 2007·Theoretical Population Biology·J M Heffernan, M J Keeling
Feb 9, 2008·Clinical Orthopaedics and Related Research·Kevin M MacDonaldJohn P Heiner
Jun 25, 2008·Briefings in Bioinformatics·Rainer BreitlingRichard Orton
Feb 9, 2010·Bioinformatics·Christian RohrMonika Heiner

❮ Previous
Next ❯

Software Mentioned

MATLAB
Snoopy
Charlie

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.

Related Papers

Advances in Experimental Medicine and Biology
Allan ClarkJane Hillston
Journal of Biomedical Informatics
Dorota FormanowiczPiotr Formanowicz
IEEE Transactions on Systems, Man, and Cybernetics. Part B, Cybernetics : a Publication of the IEEE Systems, Man, and Cybernetics Society
W T JongS M Chen
© 2021 Meta ULC. All rights reserved