CoExpNetViz takes as input a set of bait genes chosen by you and at least one pre-processed gene expression dataset. You can also specify a negative and positive cutoff value, which will be used to determine if two genes are co-expressed or not.

In short the algorithm proceeds in three big steps:

  1. The co-expression dataset is translated into a co-expression graph using the Pearson correlation coefficient and the cutoff values.
  2. Non-bait genes (or target genes) are grouped together in homologous families, which results in a graph with two types of nodes: bait genes nodes and family nodes.
  3. The family nodes are grouped into partitions if the target genes they contain are co-expressed with the same set of bait genes. The output of the algorithm is visualized in Cytoscape.

Features

  • Work on any species
  • Custom gene expression matrices
  • Plaza ortholog groups
  • Custom ortholog groups
  • Cytoscape output via web site or plugin