Dynamic identifying protein functional modules based on adaptive density modularity in protein-protein interaction networks

BMC Bioinformatics
Xianjun ShenXiaohua Hu

Abstract

The identification of protein functional modules would be a great aid in furthering our knowledge of the principles of cellular organization. Most existing algorithms for identifying protein functional modules have a common defect -- once a protein node is assigned to a functional module, there is no chance to move the protein to the other functional modules during the follow-up processes, which lead the erroneous partitioning occurred at previous step to accumulate till to the end. In this paper, we design a new algorithm ADM (Adaptive Density Modularity) to detect protein functional modules based on adaptive density modularity. In ADM algorithm, according to the comparison between external closely associated degree and internal closely associated degree, the partitioning of a protein-protein interaction network into functional modules always evolves quickly to increase the density modularity of the network. The integration of density modularity into the new algorithm not only overcomes the drawback mentioned above, but also contributes to identifying protein functional modules more effectively. The experimental result reveals that the performance of ADM algorithm is superior to many state-of-the-art protein functional modules...Continue Reading

References

Jan 15, 2003·BMC Bioinformatics·Gary D Bader, Christopher W V Hogue
Jan 23, 2003·Proceedings of the National Academy of Sciences of the United States of America·Alexander W Rives, Timothy Galitski
Dec 19, 2003·Nucleic Acids Research·H W MewesA Ruepp
Mar 5, 2004·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·M E J Newman, M Girvan
Jan 24, 2006·Nature·Anne-Claude GavinGiulio Superti-Furga
Mar 24, 2006·Nature·Nevan J KroganJack F Greenblatt
Dec 28, 2006·Proceedings of the National Academy of Sciences of the United States of America·Santo Fortunato, Marc Barthélemy
Apr 4, 2008·Journal of Biomedicine & Biotechnology·Guangyu CuiKyungsook Han
Jul 19, 2008·Bioinformatics·Jan KrumsiekRalf Zimmer
Jan 22, 2010·PLoS Computational Biology·Oron VanunuRoded Sharan
Feb 2, 2011·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Peter BoyenAalt D J van Dijk
Nov 16, 2011·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Xiao-Fei Zhang, Dao-Qing Dai
Mar 20, 2012·Nature Methods·Tamás NepuszAlberto Paccanaro
Feb 28, 2013·Science Signaling·Arunachalam VinayagamNorbert Perrimon
Feb 26, 2014·BMC Systems Biology·Hui YuZhongming Zhao
Mar 24, 2015·Scientific Reports·Chun-Yu LinJinn-Moon Yang
Jan 23, 2016·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Guoxian YuHailong Zhu

❮ Previous
Next ❯

Citations


❮ Previous
Next ❯

Software Mentioned

ClusterONE
GO
MIPS
TermFinder
MCODE
ProCope
MCL

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.