Metabolic State

Respiration Fermentation Respiration-RDR

Protein

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● P < 0.05 and |log₂(FC)| > 1

● P < 0.05

∆Molecule Across KOs. Fold changes in molecule protein abundance (mean log₂(∆gene/WT)) versus statistical significance (-log₁₀(p-value)) as quantified by LC-MS (respiration cultures) across all KOs in the study.

Pearson Coefficient | Slope

Metabolic State

Respiration Fermentation Respiration-RDR

∆Gene KO Strain #1

∆Gene KO Strain #2

Highlight Data

Shared Unique Correlated Anticorrelated Highlighting Off

KO vs KO. Comparison of fold changes in protein abundance (mean log₂(∆gene/WT)) for all proteins quantified across ∆gene1 and ∆gene1 using LC-MS (respiration cultures). The Pearson coefficient is reported here as a metric of KO-KO profile similarity.

Name	Gene Name	Systematic Name	Gene KO #1 LFQ	Gene KO #2 LFQ

 

Metabolic State

Respiration Fermentation Respiration-RDR

∆Gene KO Strain

Order

By Pearson Alphabetical

KO-KO Correlations. KO-KO profile similarities as calculated by Pearson coefficient using only significantly changing proteins (|log₂(∆gene/WT)| > 0.7 & p-value < 0.05) common to ∆gene and the compared KO as measured by LC-MS (respiration cultures). Compared KO strains with fewer than 40 proteins in common with ∆gene are not reported.

Spearman’s rank coefficient:

Metabolic State

Respiration Fermentation Respiration-RDR

Molecule vs Molecule. Comparison of fold changes in mol1 abundance vs mol2 abundance (mean log₂(∆gene/WT)) as measured by LC-MS (respiration cultures) across all KOs where both molecules were quantified. Spearman’s rank coefficient (ρ) is reported as a metric of degree of covariance. Pairs of molecules having covariance -0.58 < ρ < 0.58 are not reported here.

Metabolic State

Respiration Fermentation Respiration-RDR

Molecule

Molecule Name

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● Parent

● Protein

● Metabolite

● Lipid

▬ Positive

▬ Negative

Molecule Covariance Networks. Networks of molecules covariant with selected molecule under respiration conditions. Edges are weighted according to p-value and indicate positive/negative covariance (gray/gold). For those molecules observed to be covariant with >24 other molecules, the top 24 strongest connections to said molecule are shown.

Box Plot

Volcano

Molecule

Molecule Name

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■ RC Fold Changes

■ RD Fold Changes

RD vs RC. Box plots compare median molecule fold changes (log₂(∆gene/WT) from respiration competent (RC) ∆gene strains (left, blue) and respiration deficient (RD) ∆gene strains (right, orange). Volcano plot highlights RD vs RC response (relative to WT) for all molecules profiled under respiration conditions.