Visualizing the multiple species co-expression network

 

 

Network visualization.

 

We used VXOrd to layout the metagene co-expression network. We used the negative logarithm of the P-values of the co-expression of each pair of metagenes as the similarity measure given to the force-directed placement procedure of VXOrd.  The layout procedure situated each metagene in the X-Y plane

 

Identification of components.

 

We visually inspected the landscape produced by VXOrd and identified 12 regions of highly interconnected meta-genes that we refer to as components.  We then used a K-means clustering procedure to identify which genes were included in each of the 12 components.  Using the X-Y coordinates of the meta-genes as determined by VXOrd, we seeded the K-means procedure with 12 centers approximately equal to the locations of the 12 components.  The procedure converged in 3 iterations.  Meta-genes that were farther away than d  units from their closest center were excluded from membership in any of the 12 components.  We chose d to be 10% of the diameter of the entire landscape.