Literature DB >> 24413666

Spatiotemporal positioning of multipotent modules in diverse biological networks.

Yinying Chen1, Zhong Wang, Yongyan Wang.   

Abstract

A biological network exhibits a modular organization. The modular structure dependent on functional module is of great significance in understanding the organization and dynamics of network functions. A huge variety of module identification methods as well as approaches to analyze modularity and dynamics of the inter- and intra-module interactions have emerged recently, but they are facing unexpected challenges in further practical applications. Here, we discuss recent progress in understanding how such a modular network can be deconstructed spatiotemporally. We focus particularly on elucidating how various deciphering mechanisms operate to ensure precise module identification and assembly. In this case, a system-level understanding of the entire mechanism of module construction is within reach, with important implications for reasonable perspectives in both constructing a modular analysis framework and deconstructing different modular hierarchical structures.

Mesh:

Year:  2014        PMID: 24413666     DOI: 10.1007/s00018-013-1547-2

Source DB:  PubMed          Journal:  Cell Mol Life Sci        ISSN: 1420-682X            Impact factor:   9.261


  106 in total

1.  Protein complexes and functional modules in molecular networks.

Authors:  Victor Spirin; Leonid A Mirny
Journal:  Proc Natl Acad Sci U S A       Date:  2003-09-29       Impact factor: 11.205

2.  Evidence for dynamically organized modularity in the yeast protein-protein interaction network.

Authors:  Jing-Dong J Han; Nicolas Bertin; Tong Hao; Debra S Goldberg; Gabriel F Berriz; Lan V Zhang; Denis Dupuy; Albertha J M Walhout; Michael E Cusick; Frederick P Roth; Marc Vidal
Journal:  Nature       Date:  2004-06-09       Impact factor: 49.962

3.  Clique percolation in random networks.

Authors:  Imre Derényi; Gergely Palla; Tamás Vicsek
Journal:  Phys Rev Lett       Date:  2005-04-29       Impact factor: 9.161

4.  Modular organization of protein interaction networks.

Authors:  Feng Luo; Yunfeng Yang; Chin-Fu Chen; Roger Chang; Jizhong Zhou; Richard H Scheuermann
Journal:  Bioinformatics       Date:  2006-11-08       Impact factor: 6.937

5.  Modularity of stress response evolution.

Authors:  Amoolya H Singh; Denise M Wolf; Peggy Wang; Adam P Arkin
Journal:  Proc Natl Acad Sci U S A       Date:  2008-05-21       Impact factor: 11.205

6.  A module map showing conditional activity of expression modules in cancer.

Authors:  Eran Segal; Nir Friedman; Daphne Koller; Aviv Regev
Journal:  Nat Genet       Date:  2004-09-26       Impact factor: 38.330

7.  Enumeration of condition-dependent dense modules in protein interaction networks.

Authors:  Elisabeth Georgii; Sabine Dietmann; Takeaki Uno; Philipp Pagel; Koji Tsuda
Journal:  Bioinformatics       Date:  2009-02-11       Impact factor: 6.937

8.  GLay: community structure analysis of biological networks.

Authors:  Gang Su; Allan Kuchinsky; John H Morris; David J States; Fan Meng
Journal:  Bioinformatics       Date:  2010-12-15       Impact factor: 6.937

9.  Mendelian Inheritance in Man and its online version, OMIM.

Authors:  Victor A McKusick
Journal:  Am J Hum Genet       Date:  2007-03-08       Impact factor: 11.025

10.  An in silico method for detecting overlapping functional modules from composite biological networks.

Authors:  Ioannis A Maraziotis; Konstantina Dimitrakopoulou; Anastasios Bezerianos
Journal:  BMC Syst Biol       Date:  2008-11-01
View more
  6 in total

1.  Identify bilayer modules via pseudo-3D clustering: applications to miRNA-gene bilayer networks.

Authors:  Yungang Xu; Maozu Guo; Xiaoyan Liu; Chunyu Wang; Yang Liu; Guojun Liu
Journal:  Nucleic Acids Res       Date:  2016-08-02       Impact factor: 16.971

Review 2.  Dynamic multiprotein assemblies shape the spatial structure of cell signaling.

Authors:  Ruth Nussinov; Hyunbum Jang
Journal:  Prog Biophys Mol Biol       Date:  2014-07-18       Impact factor: 3.667

3.  Met-Controlled Allosteric Module of Neural Generation as A New Therapeutic Target in Rodent Brain Ischemia.

Authors:  Kang-Ning Li; Ying-Ying Zhang; Ya-Nan Yu; Hong-Li Wu; Zhong Wang
Journal:  Chin J Integr Med       Date:  2019-08-15       Impact factor: 1.978

4.  Quantitative assessment of gene expression network module-validation methods.

Authors:  Bing Li; Yingying Zhang; Yanan Yu; Pengqian Wang; Yongcheng Wang; Zhong Wang; Yongyan Wang
Journal:  Sci Rep       Date:  2015-10-16       Impact factor: 4.379

5.  Network-Wide Screen Identifies Variation of Novel Precise On-Module Targets Using Conformational Modudaoism.

Authors:  Bing Li; Jun Liu; Yanan Yu; Pengqian Wang; Yingying Zhang; Xumin Ni; Qiong Liu; Xiaoxu Zhang; Zhong Wang; Yongyan Wang
Journal:  CPT Pharmacometrics Syst Pharmacol       Date:  2017-11-20

6.  Mining the Synergistic Core Allosteric Modules Variation and Sequencing Pharmacological Module Drivers in a Preclinical Model of Ischemia.

Authors:  Yingying Zhang; Zide Zhao; Yanan Yu; Jun Liu; Pengqian Wang; Bing Li; Xiaoxu Zhang; Yinying Chen; Zhong Wang
Journal:  CPT Pharmacometrics Syst Pharmacol       Date:  2018-03-14
  6 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.