Skip to main content

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

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

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 noa yes
Phenotype association   yes yes yes no
Hub gene detection   yes yesb yesc 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 yesd no noe
  1. As some differences remain under the same labels, details are provided about their content
  2. aCEMiTool allows network visualization only if a protein-protein interaction network file is provided
  3. bWGCNA only provides a single hub gene selection by module
  4. cCEMiTool persistently provides the top 10 hub genes independently of the module size or connectivity
  5. dWGCNA’s differential co-expression does not correct for multiple testing
  6. ewTO have no differential co-expression method available but provides a consensus network method