Integrative analysis of human protein, function and disease networks

Scientific Reports
Wei LiuXiaofan Wang

Abstract

Protein-protein interaction (PPI) networks serve as a powerful tool for unraveling protein functions, disease-gene and disease-disease associations. However, a direct strategy for integrating protein interaction, protein function and diseases is still absent. Moreover, the interrelated relationships among these three levels are poorly understood. Here we present a novel systematic method to integrate protein interaction, function, and disease networks. We first identified topological modules in human protein interaction data using the network topological algorithm (NeTA) we previously developed. The resulting modules were then associated with functional terms using Gene Ontology to obtain functional modules. Finally, disease modules were constructed by associating the modules with OMIM and GWAS. We found that most topological modules have cohesive structure, significant pathway annotations and good modularity. Most functional modules (70.6%) fully cover corresponding topological modules, and most disease modules (88.5%) are fully covered by the corresponding functional modules. Furthermore, we identified several protein modules of interest that we describe in detail, which demonstrate the power of our integrative approach. This...Continue Reading

References

Dec 11, 1999·Nucleic Acids Research·M Kanehisa, S Goto
Jun 20, 2000·Neurobiology of Aging·H AkiyamaT Wyss-Coray
Dec 26, 2001·Nucleic Acids Research·Ada HamoshVictor A McKusick
Mar 28, 2002·Nucleic Acids Research·A J EnrightC A Ouzounis
Jan 10, 2003·Nucleic Acids Research·Gary D BaderChristopher W V Hogue
Dec 19, 2003·Nucleic Acids Research·Lukasz SalwinskiDavid Eisenberg
Mar 5, 2004·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·M E J Newman, M Girvan
Mar 30, 2004·Proteomics·Soon-Hyung YookAlbert-László Barabási
Jul 14, 2006·Bioinformatics·Jingchun Chen, Bo Yuan
Mar 14, 2007·Molecular Systems Biology·Roded SharanRon Shamir
May 16, 2007·Proceedings of the National Academy of Sciences of the United States of America·Kwang-Il GohAlbert-László Barabási
Mar 29, 2008·American Journal of Human Genetics·Sebastian KöhlerPeter N Robinson
Nov 8, 2008·Nucleic Acids Research·T S Keshava PrasadAkhilesh Pandey
Jan 10, 2009·Nature Protocols·Da Wei HuangRichard A Lempicki
Jul 15, 2009·Methods in Molecular Biology·Huaiyu Mi, Paul Thomas
Oct 24, 2009·Nucleic Acids Research·B ArandaH Hermjakob
Nov 4, 2009·Nucleic Acids Research·Andreas RueppH-Werner Mewes
Nov 10, 2009·Nucleic Acids Research·Arnaud CeolGianni Cesareni
Feb 4, 2010·PLoS Computational Biology·Stefan PinkertJörg Reichardt
Jul 24, 2010·BMC Systems Biology·Anna C F LewisCharlotte M Deane
Aug 7, 2010·Database : the Journal of Biological Databases and Curation·Marilyn SafranDoron Lancet
Nov 12, 2010·Nucleic Acids Research·David CroftLincoln Stein
Nov 13, 2010·Nucleic Acids Research·Chris StarkMike Tyers
Dec 18, 2010·Nature Reviews. Genetics·Albert-László BarabásiJoseph Loscalzo
Jan 15, 2011·Nature Reviews. Immunology·Marc Y Donath, Steven E Shoelson
Mar 19, 2011·Cell·Marc VidalAlbert-László Barabási
Jul 19, 2011·Briefings in Functional Genomics·Xiujuan WangHaiyuan Yu
Feb 22, 2012·PloS One·Martin H SchaeferMiguel A Andrade-Navarro
Jul 24, 2012·Circulation Research·Stephen Y Chan, Joseph Loscalzo
Oct 16, 2012·Briefings in Functional Genomics·Kwang-Il Goh, In-Geol Choi
Nov 30, 2012·Nucleic Acids Research·Tanya BarrettAlexandra Soboleva
Dec 12, 2012·Trends in Genetics : TIG·Laura I Furlong
Jan 10, 2013·PLoS Computational Biology·Martin H SchaeferMiguel A Andrade-Navarro
Apr 16, 2013·Database : the Journal of Biological Databases and Curation·Noa RappaportDoron Lancet
Jul 16, 2013·Scientific Reports·Juyong LeeJooyoung Lee
Nov 10, 2013·Methods in Molecular Biology·Andrei L TurinskyShoshana J Wodak
Nov 16, 2013·Scientific Reports·Marinka ŽitnikNataša Pržulj

❮ Previous
Next ❯

Citations

Apr 5, 2019·Molecular Genetics and Genomics : MGG·Asim Bikas Das
Jun 5, 2020·PLoS Computational Biology·Abolfazl Ramezanpour, Alireza Mashaghi
Mar 23, 2017·Frontiers in Genetics·Lin ChenSeyed M Moghadas
Oct 15, 2019·Frontiers in Genetics·Yu YangHaining Zhang
Jun 15, 2018·NPJ Systems Biology and Applications·Ruth StoneyJean-Marc Schwartz
May 20, 2018·Physical Review. E·Alireza Mashaghi, Abolfazl Ramezanpour
Nov 25, 2020·Diagnostics·Abolfazl RamezanpourAlireza Mashaghi

❮ Previous
Next ❯

Software Mentioned

NeTA
MCL
Bingo
DAVID
Cytoscape
RW
GeneCards
IRefWeb
Diseasome
MalaCards

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.