GIANT: A Cytoscape Plugin for Modular Networks

被引：39

作者：

Cumbo, Fabio ^{[1
]}

Paci, Paola ^{[1
,2
,3
]}

Santoni, Daniele ^{[1
]}

Di Paola, Luisa ^{[4
]}

Giuliani, Alessandro ^{[5
]}

机构：

[1] CNR, Inst Syst Anal & Comp Sci Antonio Ruberti, Rome, Italy

[2] SysBio Ctr Syst Biol, Milan, Italy

[3] SysBio Ctr Syst Biol, Rome, Italy

[4] Univ CAMPUS BioMed, Fac Engn, Rome, Italy

[5] Ist Super Sanita, Environm & Hlth Dept, I-00161 Rome, Italy

来源：

PLOS ONE | 2014年 / 9卷 / 10期

关键词：

GRAPH-THEORY; PROTEIN; HEMOGLOBIN; CENTRALITY; PARADIGM;

D O I：

10.1371/journal.pone.0105001

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Network analysis provides deep insight into real complex systems. Revealing the link between topological and functional role of network elements can be crucial to understand the mechanisms underlying the system. Here we propose a Cytoscape plugin (GIANT) to perform network clustering and characterize nodes at the light of a modified Guimera-Amaral cartography. This approach results into a vivid picture of the a topological/functional relationship at both local and global level. The plugin has been already approved and uploaded on the Cytoscape APP store.

引用

页数：7

共 25 条

[1] [Anonymous], 1985, Cambridge studies in advanced mathematics
[2] Emergence of scaling in random networks
Barabási, AL
Albert, R
[J]. SCIENCE, 1999, 286 (5439) : 509 - 512
[3] Adaptive reconfiguration of fractal small-world human brain functional networks
Bassettt, Danielle S.
Meyer-Lindenberg, Andreas
Achard, Sophie
Duke, Thomas
Bullmore, Edward T.
[J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2006, 103 (51) : 19518 - 19523
[4] Structure and dynamics of molecular networks: A novel paradigm of drug discovery A comprehensive review
Csermely, Peter
Korcsmaros, Tamas
Kiss, Huba J. M.
London, Gabor
Nussinov, Ruth
[J]. PHARMACOLOGY & THERAPEUTICS, 2013, 138 (03) : 333 - 408
[5] Shedding light on protein-ligand binding by graph theory: The topological nature of allostery
De Ruvo, Micol
Giuliani, Alessandro
Paci, Paola
Santoni, Daniele
Di Paola, Luisa
[J]. BIOPHYSICAL CHEMISTRY, 2012, 165 : 21 - 29
[6] Protein Contact Networks: An Emerging Paradigm in Chemistry
Di Paola, L.
De Ruvo, M.
Paci, P.
Santoni, D.
Giuliani, A.
[J]. CHEMICAL REVIEWS, 2013, 113 (03) : 1598 - 1613
[7] Dongen SV, 1997, THESIS U UTRECHT NET
[8] The Grapevine Expression Atlas Reveals a Deep Transcriptome Shift Driving the Entire Plant into a Maturation Program
Fasoli, Marianna
Dal Santo, Silvia
Zenoni, Sara
Tornielli, Giovanni Battista
Farina, Lorenzo
Zamboni, Anita
Porceddu, Andrea
Venturini, Luca
Bicego, Manuele
Murino, Vittorio
Ferrarini, Alberto
Delledonne, Massimo
Pezzotti, Mario
[J]. PLANT CELL, 2012, 24 (09) : 3489 - 3505
[9] Functional cartography of complex metabolic networks
Guimerà, R
Amaral, LAN
[J]. NATURE, 2005, 433 (7028) : 895 - 900
[10] The worldwide air transportation network:: Anomalous centrality, community structure, and cities' global roles
Guimerá, R
Mossa, S
Turtschi, A
Amaral, LAN
[J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2005, 102 (22) : 7794 - 7799

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