Table 5.

ΔrisA in modulating (Bvg-) conditions.

Cluster	risAD60N vs. WT Mod	ΔrisA vs. WT Mod	ΔrisAS vs. WT Mod	WT Non-Mod vs. Mod	risAD60N Non-Mod vs. Mod	ΔrisA Non-Mod vs. Mod	ΔrisAS Non-Mod vs. Mod	Description	Gene
a	NS	NS	NS	Down	NS	NS	NS	Vrgs not regulated by RisAS and phosphorylation of RisA in modulating (Bvg-) conditions and require RisAS and phosphorylation of RisA for modulation.	flaA (flagellar protein)
b	Down	Down	Down	Down	NS	NS	NS	Vrgs that require RisA and phosphorylation of RisA for full expression in modulating (Bvg-) conditions and require RisA and phosphorylation of RisA for modulation.	wza (Capsular polysaccharide)
c	NS	NS	NS	UP	UP	UP	UP	Vags not regulated by RisAS and phosphorylation of RisA during modulating (Bvg-) conditions and do not require RisAS and phosphorylation of RisA for maintaining an expected vag transcriptional response	ACT
d	NS	NS	NS	UP	NS	NS	NS	Vags not regulated by RisAS and phosphorylation of RisA during modulating (Bvg-) conditions but require RisAS and phosphorylation of RisA for maintaining an expected vag transcriptional response.	bdcB (GGDEF domain)

Transcriptional response of genes within clusters identified from comparisons used to evaluate the differential expression of the ΔrisA mutant in non-modulating (Bvg-) conditions. Yellow, indicates genes upregulated (Up) (log2fc > 1); blue, indicates genes downregulated (Down) (log2fc < −1); white, no significant change or NS in gene expression (log2fc < 1, but > −1).