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Protocols

Medusa specifications

Information


Unique identifier OMICS_08979
Name Medusa
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 2.0
Computer skills Medium
Version 3.0
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Georgios A. Pavlopoulos

Publications for Medusa

Medusa citations

 (13)
library_books

RNA sequencing analysis of activated macrophages treated with the anti HIV ABX464 in intestinal inflammation

2017
Sci Data
PMCID: 5644369
PMID: 29039845
DOI: 10.1038/sdata.2017.150

[…] lysis integrates several famous interaction network databases such as BIND, BioGrid and HPRD and constructs interaction networks for DEGs' coding proteins. The analysis result documents are showed by Medusa software and webpage version is presented by the report network_en.html under Figshare folder (Data Citation 1). […]

library_books

Proteomic signature of muscle fibre hyperplasia in response to faba bean intake in grass carp

2017
Sci Rep
PMCID: 5377455
PMID: 28367976
DOI: 10.1038/srep45950

[…] lly, the data of these two sets of numbers were searched in the STRING database, to restore the interaction map of these proteins. A protein–protein interaction network map was then created using the Medusa software (https://sites.google.com/site/medusa3visualization). […]

library_books

Infection with Plasmodium berghei ookinetes alters protein expression in the brain of Anopheles albimanus mosquitoes

2016
PMCID: 5057407
PMID: 27724938
DOI: 10.1186/s13071-016-1830-9

[…] cepted proteins with scores > 50 and P < 0.05.Protein interaction networks, built using the online database resource Search Tool for the Retrieval of Interacting Genes (STRING) [], were visualized by Medusa [], a Java application for visualizing and manipulating graphs of interaction. The interactions include direct (physical) and indirect (functional) associations derived from the genomic context […]

library_books

Modelling the Structure and Dynamics of Biological Pathways

2016
PLoS Biol
PMCID: 4980033
PMID: 27509052
DOI: 10.1371/journal.pbio.1002530

[…] There are a number of tools that currently support data visualisation in the context of networks and pathways, including CellDesigner [], NaviCell [], KEGG Mapper [], ReactomeFiViz [], iPath [], and Medusa []. As knowledge of biological interactions grows, there is, therefore, a need to construct better models to support these types of analysis, and we present here our approach to constructing su […]

library_books

Combined Gene Expression and RNAi Screening to Identify Alkylation Damage Survival Pathways from Fly to Human

2016
PLoS One
PMCID: 4839732
PMID: 27100653
DOI: 10.1371/journal.pone.0153970

[…] ion methods: databases, gene fusion, experiments, textmining and co-occurrence; iii) confidence level 0.700 (high)]. Network parameters were saved and the links (interaction strength) were handled by Medusa software []. Nodes colors include information on MMS-induced changes in gene expression (microarray) and gene survival role in RNAi screening. Interactomes were further analyzed by ViaComplex s […]

library_books

Comparative proteomic analysis of proteins expression changes in the mammary tissue of cows infected with Escherichia coli mastitis

2015
PMCID: 4588010
PMID: 25549220
DOI: 10.4142/jvs.2015.16.3.253

[…] were then analyzed with the KEGGSOAP package of R software. The protein-protein network was identified and graphically visualized as nodes (proteins) and edges (relationships between proteins) using Medusa software []. […]


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Medusa institution(s)
European Molecular Biology Laboratory Heidelberg, Germany; Max Delbrück Center for Molecular Medicine Berlin-Buch, Germany

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