. 2023 Sep 22;26(10):108016. doi: 10.1016/j.isci.2023.108016

Table 3.

Metrics of the transcriptomics and proteomics for the individual analyses and the differential expression and differential abundance analyses for the three strains

Omics	Metric	ΔH^a	ZZ^b	MM^c
Individual analyses

Transcriptomics	Million reads	26.3 (±2.0)	27.4 (±0.8)	26.0 (±1.1)
	Number of CDSs found (%)	1697/1796 (94.48%)	1699/1804 (94.18%)	1726/1730 (99.77%)
	Average CV^dof all genes	35.03	33.07	26.60
	Percent of genes with CV^dvalues ≤ 20%	44.12	39.61	26.83
Proteomics	Number of proteins found (%)	1406/1796 (78.29%)	1440/1804 (79.82%)	1374/1730 (79.42%)
	Average CV^eof all proteins	11.37	18.73	15.51
	Percent of proteins with CV^evalues ≤ 20%⁸	88.35	66.48	77.72

Omics	Metric	MM vs. ΔH	ZZ vs. ΔH	ZZ vs. MM
Differential analyses

Transcriptomics	DE^fgenes (range of log₂FC)	1482 (−13.1 to 17.8)	816 (−17.0 to 13.8)	1498 (−14.1 to 16.7)
	DE genes with \|log₂FC\| ≥ 2	975	265	1001
	DE genes that map to a reaction in the GEM	469	249	484
Proteomics	DA^gproteins (range of log₂FC)	121 (−6.6 to 6.6)	91 (−6.6 to 6.6)	93 (−6.0 to 5.9)
	DA proteins with \|log₂FC\| ≥ 2	103	59	35
	DA proteins that map to a reaction in the GEM	43	17	38
Transcriptomics + Proteomics	Fraction of DA proteins that were also DE genes	110/121 (91%)	45/91 (50%)	90/102 (88%)

Statistical significance was determined by an adjusted p-value ≤0.05. The standard deviation (±) was calculated based on the entire population.

ΔH, M. thermautotrophicus ΔH.

ZZ, M. thermautotrophicus Z-245.

MM, M. marburgensis Marburg.

Coefficient of variance (CV) values for the transcriptomics data were calculated using transcripts per million (TPM) values and can be found in Sheets 1–3 of Data S4 and Figure S6B.

Coefficient of variance (CV) values for the proteomics data were calculated using iBAQ values and can be found in Sheets 7–9 of Data S4 and Figure S6B.

DE, differential expression.

DA, differential abundance.