The analysis was performed between the following WT and mutant pairs at 22 oC : Col-0 vs prr579, Col-0 vs hsfQk and Ler vs phyAphyB. Prior to each analysis, lowly or un-expressed genes across both samples were removed. The criteria for removal each sample included: [1] rowSum(TPM_jt) < 7 x nt_j x 1.05 (TPM_jt is TPM value and n^T_j the total number of time-points for gene j at timepoint t) and [2] genes that had <5 time-points where the TPM_j < 7. Differential expression analysis of of gene was performed based on the timecourse using the odp method from the package edge (R Bioconductor) (CITE). Significant genes were chosen based on having an adjusted p-value (q-value) < 0.05.