Uncovering packaging features of co-regulated modules based on human protein interaction and transcriptional regulatory networks.

BMC Bioinformatics
Lina ChenXia Li

Abstract

Network co-regulated modules are believed to have the functionality of packaging multiple biological entities, and can thus be assumed to coordinate many biological functions in their network neighbouring regions. Here, we weighted edges of a human protein interaction network and a transcriptional regulatory network to construct an integrated network, and introduce a probabilistic model and a bipartite graph framework to exploit human co-regulated modules and uncover their specific features in packaging different biological entities (genes, protein complexes or metabolic pathways). Finally, we identified 96 human co-regulated modules based on this method, and evaluate its effectiveness by comparing it with four other methods. Dysfunctions in co-regulated interactions often occur in the development of cancer. Therefore, we focussed on an example co-regulated module and found that it could integrate a number of cancer-related genes. This was extended to causal dysfunctions of some complexes maintained by several physically interacting proteins, thus coordinating several metabolic pathways that directly underlie cancer.

References

Feb 9, 2002·Journal of Cellular Biochemistry·Shailesh K Choudhary, Rong Li
Mar 28, 2002·Nucleic Acids Research·A J EnrightC A Ouzounis
Apr 23, 2002·Nature Genetics·Nabil GuelzimFrançois Képès
May 4, 2002·Science·Sergei Maslov, Kim Sneppen
Jun 12, 2002·Molecular Biology of the Cell·Michael L WhitfieldDavid Botstein
Jan 10, 2003·Nucleic Acids Research·V MatysE Wingender
Jul 2, 2003·Molecular & Cellular Proteomics : MCP·Julio E CelisFritz E Rank
Dec 19, 2003·Nucleic Acids Research·H W MewesA Ruepp
Dec 19, 2003·Nucleic Acids Research·Suraj PeriAkhilesh Pandey
Mar 3, 2004·Nature Reviews. Cancer·P Andrew FutrealMichael R Stratton
Apr 14, 2004·Proceedings of the National Academy of Sciences of the United States of America·Esti Yeger-LotemHanah Margalit
Sep 28, 2004·Nature Genetics·Eran SegalAviv Regev
Nov 30, 2004·Science·Insuk LeeEdward M Marcotte
Jan 7, 2005·The FEBS Journal·Julio E CelisPavel Gromov
Feb 3, 2005·Proceedings of the National Academy of Sciences of the United States of America·Roded SharanTrey Ideker
May 28, 2005·Nature Genetics·Eran SegalDaphne Koller
Sep 24, 2005·BMC Bioinformatics·Ron ShamirRan Elkon
Oct 29, 2005·Journal of Cell Science·Réka Albert
Dec 31, 2005·Nucleic Acids Research·H W MewesV Stümpflen
Feb 21, 2006·Cancer Research·Dafna TsafrirDaniel A Notterman
Apr 19, 2006·Cancer Research·Astrid LièvrePierre Laurent-Puig
Sep 27, 2006·The American Journal of Surgical Pathology·Hélène BlonsClaire Danel
Oct 18, 2007·Molecular Systems Biology·Han-Yu ChuangTrey Ideker
Dec 20, 2007·Molecular Systems Biology·Qinghua CuiEdwin Wang
Dec 22, 2007·Journal of Cutaneous Pathology·Sarah E GrayMohamed Mabruk
Dec 26, 2007·Nucleic Acids Research·H W MewesT Rattei
Oct 23, 2008·Nucleic Acids Research·Lars J JensenChristian von Mering
Jan 10, 2009·Nature Protocols·Da Wei HuangRichard A Lempicki
Feb 19, 2009·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Hagit SchayekHaim Werner
Jul 25, 2009·International Journal of Cancer. Journal International Du Cancer·Yun-Ling ZhengCurtis C Harris
Aug 28, 2012·The Journal of Molecular Diagnostics : JMD·Yan JiaMingzhou Guo

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Citations

Dec 12, 2012·Omics : a Journal of Integrative Biology·Chenchen FengWeiming He
Nov 15, 2011·Molecular BioSystems·Richard S JudsonFathi Elloumi
Oct 23, 2016·Journal of Immunological Methods·Archana Prabahar, Jeyakumar Natarajan
Apr 13, 2018·GigaScience·Georgios A PavlopoulosPantelis G Bagos

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