Table 2.

Differential Gene Expression

	Early peak	Intermediate peak	Late peak	Late induction	Early repression	Late repression	none
Early peak	333	17	0	1	0	8	1
Early induction	49	33	1	9	0	0	0
Intermediate induction	5	315	17	211	0	0	1
Late induction	0	7	0	28	1	0	0
Early repression	0	0	0	1	209	30	4
Late repression	28	0	0	0	1	1022	3
none	1315	1398	395	2937	3986	3072	20,043

Distribution of differentially expressed (DE) genes in RNA-Seq clusters (columns) and microarray clusters [9] (rows). Overall, the two analyses provide similar results, but the RNA-Seq approach detects many more DE genes. Essentially all microarray DE genes were found by RNA-Seq. The main qualitative difference is that the genes in the microarray Intermediate induction cluster are now found in one or the other of 2 RNA-Seq clusters: Intermediate peak or Late induction. See Methods for details of the analysis