Network-level analysis of metabolic regulation in the human red blood cell using random sampling and singular value decomposition

BMC Bioinformatics
Christian L BarrettBernhard Ø Palsson

Abstract

Extreme pathways (ExPas) have been shown to be valuable for studying the functions and capabilities of metabolic networks through characterization of the null space of the stoichiometric matrix (S). Singular value decomposition (SVD) of the ExPa matrix P has previously been used to characterize the metabolic regulatory problem in the human red blood cell (hRBC) from a network perspective. The calculation of ExPas is NP-hard, and for genome-scale networks the computation of ExPas has proven to be infeasible. Therefore an alternative approach is needed to reveal regulatory properties of steady state solution spaces of genome-scale stoichiometric matrices. We show that the SVD of a matrix (W) formed of random samples from the steady-state solution space of the hRBC metabolic network gives similar insights into the regulatory properties of the network as was obtained with SVD of P. This new approach has two main advantages. First, it works with a direct representation of the shape of the metabolic solution space without the confounding factor of a non-uniform distribution of the extreme pathways and second, the SVD procedure can be applied to a very large number of samples, such as will be produced from genome-scale networks. These...Continue Reading

References

Jan 9, 1990·Journal of Theoretical Biology·A Joshi, B O Palsson
May 16, 1998·Proceedings of the National Academy of Sciences of the United States of America·C H Schilling, B O Palsson
May 1, 1999·Bioinformatics·T PfeifferS Schuster
Apr 6, 2001·Biotechnology and Bioengineering·C H SchillingB Ø Palsson
Apr 11, 2001·Bioinformatics·N JamshidiB O Palsson
Jun 25, 2002·Biophysical Journal·Daniel A BeardHong Qian
Jul 13, 2002·Biotechnology and Bioengineering·Ross CarlsonFriedrich Srienc
Jul 19, 2002·Biophysical Journal·Sharon J Wiback, Bernhard O Palsson
Nov 12, 2002·Biophysical Journal·Nathan D PriceBernhard Ø Palsson
Nov 15, 2002·Nature·Jörg StellingErnst Dieter Gilles
Dec 6, 2002·Genome Research·Jason A PapinBernhard Ø Palsson
Jan 28, 2003·Biophysical Journal·Nathan D PriceBernhard O Palsson
May 27, 2003·Trends in Biochemical Sciences·Jason A PapinBernhard O Palsson
Aug 6, 2003·Journal of Theoretical Biology·Iman Famili, Bernhard O Palsson
Oct 25, 2003·Journal of Theoretical Biology·Nathan D PriceBernhard O Palsson
Nov 17, 2004·Trends in Biochemical Sciences·Jason A PapinBernhard O Palsson
Apr 15, 2005·Biophysical Chemistry·Hong Qian, Daniel A Beard
Jan 19, 2006·Nature Reviews. Genetics·Jennifer L ReedBernhard O Palsson

❮ Previous
Next ❯

Citations

Jul 26, 2006·BMC Bioinformatics·Taner Z SenRobert L Jernigan
Dec 27, 2011·Critical Reviews in Biomedical Engineering·Mehmet A OrmanMarianthi G Ierapetritou
Aug 14, 2010·Journal of Biomedicine & Biotechnology·A De MartinoV Van Kerrebroeck
Oct 27, 2015·Frontiers in Microbiology·Neema Jamshidi, Anu Raghunathan
Mar 10, 2015·Journal of Bioinformatics and Computational Biology·Sayed-Amir Marashi, Zhaleh Hosseini
Nov 9, 2014·Human Genetics·Donald GemanLaurent Younes
Mar 1, 2017·Journal of Biomedical Informatics·Hamideh Fouladiha, Sayed-Amir Marashi
Jul 28, 2010·Biotechnology and Bioengineering·Mehmet A OrmanMarianthi G Ierapetritou
Oct 23, 2008·The Journal of Biological Chemistry·Jan Schellenberger, Bernhard Ø Palsson

❮ Previous
Next ❯

Software Mentioned

ExPas

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.