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March 30, 20260 citationsOpen Access

**The Coherent Core of the Proteome: Backward Elimination on Protein Interaction Networks Identifies Essential Genes in E. coli K-12**

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CCCamilo Cortes

Key Points

  • The study aims to identify essential genes in E. coli K-12 through analysis of protein interaction networks using the Coherence Engine.
  • Applied the Coherence Engine to the protein interaction network of E. coli K-12.
  • Used STRING interaction data and DisProt-verified intrinsically disordered protein classifications.
  • Performed statistical tests including t-test and Fisher exact test to validate findings.
  • Identified a coherent core of 420 proteins, making up 84% of the total analyzed.
  • Coherent core had a mean STRING degree of 17.4 compared to 6.4 for excluded proteins.
  • Significant enrichment for essential genes with an odds ratio of 8.09 (p = 0.006) confirmed.

Abstract

We apply the Coherence Engine — a backward elimination algorithm operating on a structural coherence matrix W — to the protein interaction network of E. coli K-12, using STRING interaction data and DisProt-verified intrinsically disordered protein (IDP) classifications. The engine identifies a coherent core of 420 proteins (84% of N=500) characterized by high network connectivity (mean STRING degree = 17. 4 vs 6. 4 for excluded proteins, t-test p < 0. 0001) and significant enrichment for essential genes (OR = 8. 09, p = 0. 006, Fisher exact test). All six pre-registered ZKP falsifiability predictions are satisfied (6/6, CM_Éter = 1. 000). The coherent core corresponds to the central metabolic infrastructure of E. coli — glycolysis, TCA cycle, respiratory chain, and ribosomal machinery — identified from network topology alone, without using biological pathway annotations as input. This result constitutes the second empirical validation of TCS universality, complementing the galactic-scale result in Cortes (2026a) where baryon-dominated galaxies form the coherent core of the SPARC rotation curve sample.

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Cite This Study

Camilo Cortes (2026) studied this question.

synapsesocial.com/papers/69c9c553f8fdd13afe0bd4edhttps://doi.org/10.5281/zenodo.19292060
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