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Table 1 Features Provided by Programs that Identify Co-Expression Modules. Over representation analysis of CoP, and GeNET programs is considered “limited” because they only allow the usage of specific gene sets (GO, Pfam or KEGG). The runtime of 2 studies using the same computer and default settings are shown for CEMiTool, WGCNA, and Petal

From: CEMiTool: a Bioconductor package for performing comprehensive modular co-expression analyses

Features CEMiTool WGCNA Petal CoP GeNET DiffCoEx CoXpress DICER DINGO
Automatic Gene Filtering yes no no no no no no no no
Over representation analysis yes yes no limited limited no no no no
Gene set enrichment analysis yes no no no yes no no no no
Integration with interactome yes no no no no no no no no
Report in HTML yes no no yes no no no no no
Native plots yes yes no no yes no no no no
Search for a gene or gene list yes no yes yes yes no no no no
Merging modules yes yes no no no yes no yes no
Allows 2+ sample groups yes yes yes yes yes no no no no
R package yes yes yes no no no yes no yes
Year of last update 2017 2017 2017 2010 Unknown Unknown 2013 Unknown Unknown
Runtime for study GSE18090 2min12s 3min10s 17min18s
Runtime for study GSE43777 3min03s 4min33s 40min10s