GWENA: gene co-expression networks analysis and extended modules characterization in a single Bioconductor package

Table 4 Key features of GWENA compared to similar tools such as WGCNA, CEMiTool and wTO

Functionnalities	Details	GWENA	WGCNA	CEMiTool	wTO
Gene set enrichment	Gene ontology	yes	yes	no	no
	Pathways (KEGG/Reactome)	yes	no	no	no
	Regulation actors (TRANSFAC/miRTarBase)	yes	no	no	no
	Protein databases (Human Protein Atlas/CORUM)	yes	no	no	no
	Custom GMT import	yes	no	yes	no
Native network visualization		yes	no	no^a	yes
Phenotype association		yes	yes	yes	no
Hub gene detection		yes	yes^b	yes^c	no
Igraph compatibility for extended topology metrics calculation		yes	no	no	no
Sub-module detections inside module & graph coloration accordingly		yes	no	no	no
Modules differential co-expression		yes	yes^d	no	no^e

As some differences remain under the same labels, details are provided about their content
^aCEMiTool allows network visualization only if a protein-protein interaction network file is provided
^bWGCNA only provides a single hub gene selection by module
^cCEMiTool persistently provides the top 10 hub genes independently of the module size or connectivity
^dWGCNA’s differential co-expression does not correct for multiple testing
^ewTO have no differential co-expression method available but provides a consensus network method

ISSN: 1471-2105