Table 1.

Computational tools for active module identification.

nameYearReferenceTypeNote
JActiveModules2002Ideker et al (2002)Cytoscape pluginOK
GiGA2004Breitling et al (2004)cmdOK
SAMBA2004Tanay et al (2004)gui/cmdExecution error
GXNA2007Nacu et al (2007)cmdBroken link
MATISSE2007Ulitsky and Shamir (2007)guiDifficult to usea
PinnacleZ2007Chuang et al (2007)Cytoscape pluginDifficult to useb
CEZANNE2009Ulitsky and Shamir (2009)guiDifficult to usea
BioNet2010Beisser et al (2010)cmdDifficult to usec
RegMOD2010Qiu et al (2010)cmdNot free to used
ClustEx22010Gu et al (2010)cmdOK
RME2011Miller et al (2011)cmdNot for transcriptomics datae
COSINE2011Ma et al (2011)cmdDifficult to usef,g
EnrichNet2012Glaab et al (2012)cmdUnable to run on drosophila data
MEMo2012Ciriello et al (2012)cmdDifficult to useh
BMRF-net2013Chen et al (2013)Cytoscape pluginDifficult to useb
Walktrap-gm2013Petrochilos et al (2013)cmdInstallation failure
TimeXNet2014Patil and Nakai (2014)web/gui/cmdNo resultsi
WMAXC2014Amgalan and Lee (2014)cmdBroken link
DIAMOnD2015Ghiassian et al (2015)cmdOKg
Hotnet22015Leiserson et al (2015)cmdDifficult to usej
GLADIATOR2017Silberberg et al (2017)cmdNot for transcriptomics datak
MOEA2017Chen et al (2017)cmdNot free to used
MRF2017Robinson et al (2017)cmdNot free to used
ModuleDiscoverer2018Vlaic et al (2018)cmdBroken link
ResponseNet2019Basha et al (2019)webNo resultsi
AMINE2021Pasquier et al (2021) PreprintwebOK
  • a Program written in Java 5 with a graphical interface based on Swing whose development was abandoned when Java 8 appeared in 2014.

  • b Not available for Cytoscape 3.

  • c Require to execute a dozen of lines to process the example data included with the program.

  • d Need MATLAB which is not free.

  • e The method identifies patterns of recurrent genomic aberration in tumor samples.

  • f Requires to execute multiple commands in R language, in particular it is necessary to compute a matrix containing the differential correlation between each pair of connected nodes on the network.

  • g Identifies only one module.

  • h The documentation contains the following warning: Generating the files needed by the program may require a fair amount of work, as several of them are the results of other algorithms.

  • i The program ran for several hours without providing any results.

  • j Requires to execute multiples commands ; the script used to analyze data of the associated paper is 68 lines long.

  • k The aim of the program is to identify relationship between diseases modules ; user need to suply known genes associated with diseases.