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. 2015 Feb;16(1):3–22. doi: 10.2174/1389202915666141110210634

Table 1.

Some available strategies and their representative methods for inferring regulatory networks from gene expression profiles. Their supporting websites and original publications are also shown. Some R packages (http://cran.r-project.org) for Bayesian learning and differential equation parameter identification are also shown. In each category, the methods are ordered alphabetically.

Category Method Website Reference
Correlation-based methods ANOVA http://www2.bio.ifi.lmu.de/˜kueffner/anova.tar.gz [155]
ARACNE http://wiki.c2b2.columbia.edu/califanolab/ index.php/Software/ARACNE [56, 73]
CLR http://cran.r-project.org/web/packages/parmigene [74]
C3NET http://cran.r-project.org/web/packages/c3net/index.html [71]
GLMNET http://cran.r-project.org/web/packages/glmnet/ [99, 100]
grangerTlasso http://www.biostat.washington.edu/~ashojaie/ [103]
MINET http://cran.r-project.org/web/packages/minet/ [76]
MRNET http://penglab.janelia.org/proj/mRMR/ [75]
ParCorA http://www.comp-sys-bio.org/software.html [88]
PCA-CMI http://csb.shu.edu.cn/subweb/grn.htm [60]
Relevance Network http://buttelab.stanford.edu/start [65, 70]
Schafer and Strimmer http://strimmerlab.org/software.html [89]
Simone http://cran.r-project.org/web/packages/simone/ [156]
Stuart et al. http://cmgm.stanford.edu/~kimlab/multispecies/ [64]
WGCNA http://labs.genetics.ucla.edu/horvath/ CoexpressionNetwork/Rpackages/ WGCNA [66, 68]
Boolean network methods Akutsu et al. http://www.bic.kyoto-u.ac.jp/takutsu/members/takutsu/ [106, 109]
Antelope http://turing.iimas.unam.mx:8080/AntelopeWEB/content/about.jsp [157]
BoolNet http://cran.r-project.org/web/packages/BoolNet [158]
BooleSim https://github.com/matthiasbock/BooleSim [159]
Handorf and Klipp http://code.google.com/p/libscopes/wiki/Paper2011 [160]
Modent http://acgt.cs.tau.ac.il/modent/ [161]
REVEAL Not available [105]
Shmulevich et al. http://shmulevich.systemsbiology.net/ [112, 113, 115]
Bayesian network methods ARTIVA http://cran.r-project.org/web/packages/ARTIVA/index.html [162]
BC3NET http://cran.r-project.org/web/packages/bc3net/index.html [151]
Beal et al. http://www.cse.buffalo.edu/faculty/mbeal/ [125]
BNFinder http://bioputer.mimuw.edu.pl/software/bnf [163]
BNLEARN http://cran.r-project.org/web/packages/bnlearn [164]
BNT http://code.google.com/p/bnt/ [120]
Frideman et al. http://www.cs.huji.ac.il/labs/compbio/expression/ [117, 119]
GeneNet http://cran.r-project.org/web/packages/GeneNet [83]
G1DBN http://cran.r-project.org/web/packages/G1DBN/index.html [165]
GlobalMIT https://code.google.com/p/globalmit [166]
Module network http://ai.stanford.edu/~erans/module_nets/ [84]
TESLA http://sailing.cs.cmu.edu/tesla/index.html [126]
SSM http://www.chems.msu.edu/groups/chan/ssm.zip [167]
Differential equation methods Chen et al. Not available [127]
deSolve http://cran.r-project.org/web/packages/deSolve [168]
D'haeseleer et al. Not available [95]
D-NetWeaver https://cbim.urmc.rochester.edu/software/d-netweaver/ [128, 129]
GRNInfer http://doc.aporc.org/wiki/Software [41]
Inferelator http://bonneaulab.bio.nyu.edu/software.html [154]
Tegner et al. http://www.bu.edu/bme/people/primary/collins/ [34, 36]
TRNInfer http://www.sysbio.ac.cn/cb/chenlab/software.htm [153]
Wahde and Hertz http://www.nbi.dk/~hertz/ [169]
Knowledge-based methods Banjo http://www.cs.duke.edu/~amink/software/banjo [142]
BNP http://research.bioe.bilgi.edu.tr/bnp/ [170]
Greenfield et al. http://bonneaulab.bio.nyu.edu/software.html [171]
Hill et al. http://mukherjeelab.nki.nl/DBN [172]
Linear programming http://doc.aporc.org/wiki/Software [138]
Liu et al. http://doc.aporc.org/wiki/Software [134]
Network energy Not available [139, 143]
Network Screening http://www.molprof.jp/~horimoto/ [144]
PLASSO http://nba.uth.tmc.edu/homepage/liu/pLasso [173]
Miscellaneous methods GENIE3 http://homepages.inf.ed.ac.uk/vhuynht/software.html [152]
Neural network http://www.me.chalmers.se/~mwahde [174]
Petri net http://dnagarden.hgc.jp/en/doku.php/software [175]
Supervised learning http://cbio.ensmp.fr/sirene [167, 177]
TIGRESS http://cbio.ensmp.fr/tigress [178]
Differential equation methods Chen et al. Not available [127]
deSolve http://cran.r-project.org/web/packages/deSolve [168]
D'haeseleer et al. Not available [95]
D-NetWeaver https://cbim.urmc.rochester.edu/software/d-netweaver/ [128, 129]
GRNInfer http://doc.aporc.org/wiki/Software [41]
Inferelator http://bonneaulab.bio.nyu.edu/software.html [154]
Tegner et al. http://www.bu.edu/bme/people/primary/collins/ [34, 36]
TRNInfer http://www.sysbio.ac.cn/cb/chenlab/software.htm [153]
Wahde and Hertz http://www.nbi.dk/~hertz/ [169]
Knowledge-based methods Banjo http://www.cs.duke.edu/~amink/software/banjo [142]
BNP http://research.bioe.bilgi.edu.tr/bnp/ [170]
Greenfield et al. http://bonneaulab.bio.nyu.edu/software.html [171]
Hill et al. http://mukherjeelab.nki.nl/DBN [172]
Linear programming http://doc.aporc.org/wiki/Software [138]
Liu et al. http://doc.aporc.org/wiki/Software [134]
Network energy Not available [139, 143]
Network Screening http://www.molprof.jp/~horimoto/ [144]
PLASSO http://nba.uth.tmc.edu/homepage/liu/pLasso [173]
Miscellaneous methods GENIE3 http://homepages.inf.ed.ac.uk/vhuynht/software.html [152]
Neural network http://www.me.chalmers.se/~mwahde [174]
Petri net http://dnagarden.hgc.jp/en/doku.php/software [175]
Supervised learning http://cbio.ensmp.fr/sirene [176, 177]
TIGRESS http://cbio.ensmp.fr/tigress [178]