Moksiskaan 2.04 – Translate Gene Sets to Networks

Moksiskaan 2.04

:: DESCRIPTION

Moksiskaan is a generic database that can be used to integrate information about the connections between genes, proteins, pathways, drugs, and other biological entities. Moksiskaan provides various pathway components for Anduril and may be used to extends its capabilities.

::DEVELOPER

Hautaniemi Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Moksiskaan

:: MORE INFORMATION

Citation

Marko Laakso and Sampsa Hautaniemi
Integrative platform to translate gene sets to networks
Bioinformatics (2010) 26 (14): 1802-1803.

VANESA 0.2 – Visualization and Analysis of Networks in System Biology

VANESA 0.2

:: DESCRIPTION

VANESA is a software application for the visualization and analysis of biomedical networks in system biology applications to create systems that can answer fundamental questions and moreover, imitate cell behavior.

::DEVELOPER

the Bioinformatics / Medical Informatics department at Bielefeld University.

:: SCREENSHOTS

VANESA

:: REQUIREMENTS

  •  Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 VANESA

:: MORE INFORMATION

Citation

VANESA – a software application for the visualization and analysis of networks in system biology applications.
Brinkrolf C, Janowski SJ, Kormeier B, Lewinski M, Hippe K, Borck D, Hofestädt R.
J Integr Bioinform. 2014 Jun 23;11(2):239. doi: 10.2390/biecoll-jib-2014-239.

ClueGO 2.0.5 – Cytoscape Plugin to Decipher Gene Ontology and Pathway Annotation Networks

ClueGO 2.0.5

:: DESCRIPTION

ClueGO is a Cytoscape plug-in that visualizes the non-redundant biological terms for large clusters of genes in a functionally grouped network and it can be used in combination with GOlorize. The identifiers can be uploaded from a text file or interactively from a network of Cytoscape. The type of identifiers supported can be easely extended by the user. ClueGO performs single cluster analysis and comparison of clusters. From the ontology sources used, the terms are selected by different filter criteria. The related terms which share similar associated genes can be fused to reduce redundancy. The ClueGO network is created with kappa statistics and reflects the relationships between the terms based on the similarity of their associated genes. On the network, the node colour can be switched between functional groups and clusters distribution. ClueGO charts are underlying the specificity and the common aspects of the biological role.

::DEVELOPER

Integrative Cancer Immunology Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 ClueGO

:: MORE INFORMATION

Citation

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks.
Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman WH, Pagès F, Trajanoski Z, Galon J.
Bioinformatics. 2009 Apr 15;25(8):1091-3. Epub 2009 Feb 23.

Pubcrawl – Networks of Literature-based Semantic Distances with Protein Domain Interactions

Pubcrawl

:: DESCRIPTION

Pubcrawl is an interactive web application that generates normalized medline distances for terms, and then returns a network topology based on the term distances and protein domain interactions.

Pubcrawl Online Version

::DEVELOPER

Shmulevich Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Pubcrawl

:: MORE INFORMATION

M-BISON 1.0 – Microarray-Based Integration of data SOurces using Networks

M-BISON 1.0

:: DESCRIPTION

M-BISON is a software to implement an efficient method for the integration of biological knowledge with microarray gene expression data to enhance identification of differentially expressed genes

::DEVELOPER

M-BISON Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 M-BISON

:: MORE INFORMATION

Citation

Bernie J Daigle Jr and Russ B Altman
M-BISON: Microarray-based integration of data sources using networks
BMC Bioinformatics 2008, 9:214