The relative vertex clustering value--a new criterion for the fast discovery of functional modules in protein interaction networks

BMC Bioinformatics
Zina M Ibrahim, Alioune Ngom

Abstract

Cellular processes are known to be modular and are realized by groups of proteins implicated in common biological functions. Such groups of proteins are called functional modules, and many community detection methods have been devised for their discovery from protein interaction networks (PINs) data. In current agglomerative clustering approaches, vertices with just a very few neighbors are often classified as separate clusters, which does not make sense biologically. Also, a major limitation of agglomerative techniques is that their computational efficiency do not scale well to large PINs. Finally, PIN data obtained from large scale experiments generally contain many false positives, and this makes it hard for agglomerative clustering methods to find the correct clusters, since they are known to be sensitive to noisy data. We propose a local similarity premetric, the relative vertex clustering value, as a new criterion allowing to decide when a node can be added to a given node's cluster and which addresses the above three issues. Based on this criterion, we introduce a novel and very fast agglomerative clustering technique, FAC-PIN, for discovering functional modules and protein complexes from a PIN data. Our proposed FAC-PIN...Continue Reading

References

Dec 11, 1999·Nature·L H HartwellA W Murray
Jun 13, 2002·Proceedings of the National Academy of Sciences of the United States of America·M Girvan, M E J Newman
Jan 15, 2003·BMC Bioinformatics·Gary D Bader, Christopher W V Hogue
Oct 1, 2003·Proceedings of the National Academy of Sciences of the United States of America·Victor Spirin, Leonid A Mirny
Feb 26, 2004·Proceedings of the National Academy of Sciences of the United States of America·Filippo RadicchiDomenico Parisi
Mar 30, 2004·Proteomics·Soon-Hyung YookAlbert-László Barabási
Jul 13, 2004·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·M E J Newman
Feb 9, 2005·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Aaron ClausetCristopher Moore
Oct 10, 2006·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·M E J Newman
Nov 8, 2006·BMC Bioinformatics·Sylvain Brohée, Jacques van Helden
Nov 10, 2006·Bioinformatics·Feng LuoRichard H Scheuermann
Dec 2, 2006·BMC Bioinformatics·Caroline C Friedel, Ralf Zimmer
Mar 31, 2007·IEEE Transactions on Nanobioscience·Pengjun Pei, Aidong Zhang
Jun 25, 2008·Journal of Bioinformatics and Computational Biology·Hon Nian ChuaLimsoon Wong
Jun 22, 2010·Nature·Yong-Yeol AhnSune Lehmann
Aug 25, 2010·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Jianxin WangYi Pan
Nov 15, 2011·Bioinformatics·Emmanuelle BeckerChristine Brun
Dec 28, 2011·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Clara Pizzuti, Simona E Rombo

❮ Previous
Next ❯

Citations

Mar 24, 2012·PloS One·Anat Lavi-ItzkovitzMike Fainzilber
Jan 10, 2013·PLoS Computational Biology·Dong-Yeon ChoTeresa M Przytycka
Apr 12, 2013·PloS One·Nathalie Villa-VialaneixMagali SanCristobal
Apr 29, 2019·BMC Bioinformatics·Sara RahiminejadShankar Subramaniam

❮ Previous
Next ❯

Software Mentioned

GN
HC
FAC
PIN
CNM
REACTOME
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.