What to do with the GEM?

The Gene Expression Matrix (GEM) created by GEMmaker can be used for either Differential Gene Expression (DGE) analyssi or Gene Co-expression Network (GCN) analysis.

DGE Analysis

The raw GEM can be used for differential gene expression (DGE) analysis in edgeR and DESeq2.

Network Analysis

The GEM can be used to construct a gene co-expression network (GCN). The most common tool for construction of GCNs is WGCNA. However, the developers of GEMmaker have also developed a new tool for constructing condition-specific GCNs called KINC. It is a high-performance application that can construct networks using Pearson or Spearman for pairwise correlation, as well as Gaussian mixture models (GMMs) for pairwise clustering. KINC is a Qt/ACE application that is capable of running on CPUs and GPUs, which means that it can scale to larger workloads.


Prior to network construction it is recommended to normalized (such as with quantile normalization) and log-transform the GEM. GEMmaker does not provide this functionality.