Genome function is organized into highly coordinated and dynamically changing networks of genes. To detect such networks among the FGFR1-controlled genes, we performed a pairwise correlation29 of all differentially regulated genes. Among 4704 genes that were regulated during NPC differentiation to NCCs, we detected groups of genes that displayed high-positive correlation (+0.9 to +1.0; changing activities in the same direction) and genes which showed high-negative correlation (−0.9 to −1.0; changing activities in opposite direction) (Supplementary Fig. 7a). In each category, the 200 most connected genes from the differentiated NCCs were analyzed using circular network graphs. A common feature of both positive and negative networks was that their top 200 coordinate genes were highly interconnected in NCCs (Supplementary Fig. 7b, c). These networks formed during NCC differentiation as they showed little or no connectivity in NPCs.
