TSN-PCD / DFM-CIN – Identify Protein Complexes / Functional Modules from these TSNs

TSN-PCD / DFM-CIN

:: DESCRIPTION

The algorithm TSN-PCD was developed to identify protein complexes from these TSNs (time-sequenced subnetworks).

DFM-CIN is proposed to discover functional modules based on the identified complexes.

::DEVELOPER

CSU-Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 TSN-PCD / DFM-CIN

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 May 23;13:109. doi: 10.1186/1471-2105-13-109.
Towards the identification of protein complexes and functional modules by integrating PPI network and gene expression data.
Li M1, Wu X, Wang J, Pan Y.

FunMod 2.8.3 – Cytoscape plugin for Identifying Functional Modules in undirected Protein-protein Networks

FunMod 2.8.3

:: DESCRIPTION

FunMod is an innovative Cytoscape version 2.8 plugin that is able to mine undirected protein-protein networks and to infer sub-networks of interacting proteins intimately correlated with relevant biological pathways.

::DEVELOPER

the Systems Biology Research Group at the Department of Control and Computer Engineering of Politecnico di Torino.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Java
  • Cytoscape

:: DOWNLOAD

 FunMod

:: MORE INFORMATION

Citation

FunMod: a Cytoscape plugin for identifying functional modules in undirected protein-protein networks.
Natale M, Benso A, Di Carlo S, Ficarra E.
Genomics Proteomics Bioinformatics. 2014 Aug;12(4):178-86. doi: 10.1016/j.gpb.2014.05.002.

ModuleSearch – Finding Functional Modules in Protein-protein Interaction Network

ModuleSearch

:: DESCRIPTION

ModuleSearch is a software for finding cliques and near-cliques in a protein-protein interaction network.

::DEVELOPER

Biocomputing Lab

:: SCREENSHOTS

ModuleSearch

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • JRE

:: DOWNLOAD

 ModuleSearch

:: MORE INFORMATION

Citation

Comput Methods Biomech Biomed Engin. 2012;15(7):691-9. doi: 10.1080/10255842.2011.555404. Epub 2011 Aug 9.
ModuleSearch: finding functional modules in a protein-protein interaction network.
Cui G1, Shrestha R, Han K.

MonaLisa r5_100 – Visualization and Analysis of Functional Modules in Biochemical Networks

MonaLisa r5_100

:: DESCRIPTION

MonaLisa is a Petri net based tool for the analysis of biochemical networks. It comprises an editor supported by an intuitive visualization and animation, and various analysis techniques, focusing on network decomposition, knockout analysis, and other. It includes the computation of elementary modes (T-invariants), P-invariants, Maximal common transition sets (MCT-sets), T-clusters, minimal cut sets (MCS), degree distribution, cluster coefficient distribution.

::DEVELOPER

Molecular Bioinformatics MolBI

:: SCREENSHOTS

MonaLisa

::REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 MonaLisa

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jun 1;29(11):1469-70. doi: 10.1093/bioinformatics/btt165. Epub 2013 Apr 5.
MonaLisa–visualization and analysis of functional modules in biochemical networks.
Einloft J, Ackermann J, Nöthen J, Koch I.

CyClus3D 3.3 – Cytoscape plugin for Identifying Functional Modules

CyClus3D 3.3

:: DESCRIPTION

CyClus3D is a Cytoscape plugin for identifying functional modules in integrated networks composed of multiple interaction types. CyClus3D operates by clustering user-defined 3-node network motifs.

::DEVELOPER

Van de Peer Lab

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 CyClus3D

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jun 1;27(11):1587-8. doi: 10.1093/bioinformatics/btr182.
CyClus3D: a Cytoscape plugin for clustering network motifs in integrated networks.
Audenaert P1, Van Parys T, Brondel F, Pickavet M, Demeester P, Van de Peer Y, Michoel T.

MATISSE 1.1 – Detection of Functional Modules using Interaction Networks and Expression data

MATISSE 1.1

:: DESCRIPTION

MATISSE (Module Analysis via Topology of Interactions and Similarity SEts) is a program for detection of functional modules using interaction networks and expression data. A functioncal module is a group of cellular components and their interactions that can be attributed a specific biological function.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

::REQUIREMENTS

  • Windows/Linux
  • Java

:: DOWNLOAD

 MATISSE

:: MORE INFORMATION

Citation

Identification of functional modules using network topology and high-throughput data
I. Ulitsky and R. Shamir
BMC Systems Biology, Vol. 1, No. 8 (2007)