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Fig. 1 | BMC Bioinformatics

Fig. 1

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

Fig. 1

Detailed steps of analysis performed in GWENA’s pipeline, from expression data to characterization of the modules and comparison of conditions. Input : expression matrix pre-normalized and aggregated to gene level if it is a transcript matrix. Filtering : optional genes filtration according to transcriptomic input technology. Co-expression network construction : computation through modified WGCNA function of a correlation matrix on the gene expression matrix, then transformation into an adjacency matrix, and finally into a topological overlap matrix (TOM). Modules detection : genes clusterization over the TOM with another modified WGCNA function. Biological integration : gene set enrichment of each module using g:Profiler services, and phenotypic association if a phenotype matrix is provided to describe the samples. Graph analysis : transformation of the TOM in a graph to compute different topological metrics, detect the hub genes, and detect sub-modules of one module. Modules differential co-expression over N conditions : permutation test using NetRep combined with a Z summary to detect preserved or unpreserved modules

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