What are gene co-expression networks and how are they different from PPI networks?

Gene co-expression networks are constructed by measuring the similarity (i.e. correlation) in pairwise gene expression profiles across many conditions. Two genes are connected to each other in the network if they tend to respond similarly (consistently up or down regulated together) in different conditions or perturbations. They may be co-regulated, without physical interactions.

Note some PPI databases include gene co-expression data, along with other types of evidence, to define interactions. Since co-expression networks can be computed from expression data alone, it is easier to generate separate ones for many different tissues and even cell types compared to PPI networks.

NetworkAnalyst offers two types of gene co-expression network

  • Tissue specific gene coexpression networks collected from the TCSBN database
  • Cell-specific gene coexpression networks based on Immuno-Navigator