Genome-wide gene expression and RNA half-life measurements allow predictions of regulation and metabolic behavior in Methanosarcina acetivorans

Table 3 Classification of regulation type for differentially expressed metabolic genes in the consensus set from Table 1. Metabolic genes are defined as those that are associated with a reaction in the metabolic model iST807

	Transcriptionally controlled	Shared control	Degradationally controlled	Indeterminate^b
	ρ _D≤0	0 <ρ _D<1	ρ _D≥1
Comparison	Number (%^a)	Number (%^a)	Number (%^a)	Number (%^a)
sectionMeOH vs. TMA	54 (25.6)	23 (10.9)	126 (59.7)	8 (3.8)
MeOH vs. Ace	25 (12.4)	49 (24.4)	97 (48.3)	30 (14.9)
TMA vs. Ace	107 (16.6)	149 (23.1)	320 (49.6)	69 (10.7)

^aPercentage of DEG out of those for which half-lives and RNA reads were of sufficient quality to apply the control analysis (i.e. CV <0.5). ^bRegulation coefficients could not be determined because half-life data was low quality (CV ≥0.5)

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