Table 1. Loss of HOS1 Results in Large Numbers of Upregulated Genes.

Category	Upregulated in hos1-3	Downregulated in hos1-3
Total number of genes	1308	126
Expressed C+E union	832	49
Circadian C+E union	400	35
Genes circadian expressed (%)	48.1	71.4
Differentially expressed clock genes	PRR5, PRR3, TOC1, LUX, ELF3, ELF4, CHE	None

Genes that are downregulated are also dominated by circadian-expressed genes. Analysis of RNA sequencing shows that reads map to 15,070 genes expressed in the hos1 mutant at dawn. C+E union refers to the list of circadian-expressed genes defined by Covington et al. (2008). Significant gene expression differences were calculated by Cufflinks (Trapnell et al., 2012).