|How to begin?|
|Access, users, projects|
|Identification of driver genes|
|Exploration of molecular landscapes|
|Using Venn diagrams|
|Using stand-alone software|
Potentially, you can obtain much more useful output by running the perl script NEA.pl off-line.
NEA.pl is the script that executes network enrichment analysis at this web site.
Please note that while running analysis online, on this web-site, you can both look up the command line and download specific input and output files.
Watch the text and links that appear after the current analysis finished.
You can to use them either as a reference or as input to a modified analysis off-line. _tmpAGS, _tmpFGS, and _tmpNET contain your submitted gene list(s), the collection of functional gene sets, and the network.
Ashwini Jeggari, Zhanna Alekseenko, José Dias, Johan Ericson, and Andrey Alexeyenko EviNet: a web platform for network enrichment analysis with flexible definition of gene sets Nucleic Acids Res 2018 Jul 2;46(W1):W163-W170. doi: 10.1002/1878-0261.12350.The method of network enrichment analysis (NEA):
Andrey Alexeyenko, Woojoo Lee, Maria Pernemalm, Justin Guegan, Philippe Dessen, Vladimir Lazar, Janne Lehtiö and Yudi Pawitan Network enrichment analysis: extension of gene-set enrichment analysis to gene networks BMC Bioinformatics 2012 Sep 11;13:226 doi: 10.1186/1471-2105-13-226.The first implementation of the fast NEA algorithm:
Andrey Alexeyenko, Deena M. Wassenberg, Edward K. Lobenhofer, Jerry Yen, Erik L.L. Sonnhammer, Elwood Linney and Joel N. Meyer Dynamic zebrafish interactome reveals transcriptional mechanisms of dioxin toxicity PLoS One 2010 May 5;5(5):e10465 doi: 10.1371/journal.pone.0010465.The back-end software:
Ashwini Jeggari and Andrey Alexeyenko NEArender: an R package for functional interpretation of ‘omics’ data via network enrichment analysis BMC Bioinformatics 2017 Mar 23;18(Suppl 5):118. doi: 10.1186/s12859-017-1534-y.