Integrative analysis of human protein, function and disease networks

Scientific Reports
Wei LiuXiaofan Wang


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


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
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