| | 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
