Predicting functional associations from metabolism using bi-partite network algorithms.

BMC Systems Biology
Balaji Veeramani, Joel S Bader

Abstract

Metabolic reconstructions contain detailed information about metabolic enzymes and their reactants and products. These networks can be used to infer functional associations between metabolic enzymes. Many methods are based on the number of metabolites shared by two enzymes, or the shortest path between two enzymes. Metabolite sharing can miss associations between non-consecutive enzymes in a serial pathway, and shortest-path algorithms are sensitive to high-degree metabolites such as water and ATP that create connections between enzymes with little functional similarity. We present new, fast methods to infer functional associations in metabolic networks. A local method, the degree-corrected Poisson score, is based only on the metabolites shared by two enzymes, but uses the known metabolite degree distribution. A global method, based on graph diffusion kernels, predicts associations between enzymes that do not share metabolites. Both methods are robust to high-degree metabolites. They out-perform previous methods in predicting shared Gene Ontology (GO) annotations and in predicting experimentally observed synthetic lethal genetic interactions. Including cellular compartment information improves GO annotation predictions but degr...Continue Reading

References

Jul 21, 2004·Bioinformatics·Koji Tsuda, William Stafford Noble
Oct 21, 2004·Nature Reviews. Microbiology·Nathan D PriceBernhard Ø Palsson
Dec 14, 2004·Nature Genetics·Daniel SegrèRoy Kishony
Aug 13, 2005·Bioinformatics·Tobias SingThomas Lengauer
Dec 31, 2005·Nucleic Acids Research·Chris StarkMike Tyers
Mar 8, 2006·BMC Bioinformatics·Scott A BeckerBernhard Ø Palsson
May 27, 2006·Molecular Systems Biology·Peter KharchenkoDennis Vitkup
Feb 8, 2007·Proceedings of the National Academy of Sciences of the United States of America·Richard HarrisonDaniela Delneri
Jan 30, 2008·PLoS Computational Biology·Richard A NotebaartBalázs Papp
Jul 5, 2008·Proceedings of the National Academy of Sciences of the United States of America·D-S LeeA-L Barabási
Feb 6, 2009·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Balaji Veeramani, Joel S Bader
Apr 30, 2010·BMC Bioinformatics·Jan SchellenbergerBernhard Ø Palsson
Apr 17, 2013·BMC Systems Biology·S Alexander RiemerDietmar Schomburg

❮ Previous
Next ❯

Methods Mentioned

BETA
interaction prediction

Software Mentioned

COBRA MATLAB
Cobra Toolbox
ROCR
R

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.