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EGFR Integrative Proteogenomics

Planning complete · scaffolding in progress

The research question

Ten-module computational study of human EGFR (UniProt P00533): evolutionary conservation, transcriptomics, PTM network, re-analysis of public PRIDE proteomics data, structural characterization, and the mechanism of clinical resistance mutations (L858R, T790M; erlotinib → osimertinib).

Target: a bioRxiv preprint.

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Current status

No analysis results yet. No preprint. bioRxiv is a target.

What is planned

  1. Repository scaffolding

    in progress

    reproducible repository layout, pinned environment, and a shared analysis package.

  2. Sequence annotation

    planned

    domain, topology and variant map of UniProt P00533, used as the coordinate frame for all later modules.

  3. Structural characterization

    planned

    inactive versus active kinase structures, ectodomain dimerization, and AlphaFold models benchmarked against experimental structures.

  4. Mutation analysis

    planned

    the structural and energetic basis of L858R, T790M and C797S, with a second-method cross-check.

  5. PTM network

    planned

    the six C-terminal autophosphorylation tyrosines and the effectors they recruit.

  6. Transcriptomic validation

    planned

    the EGF and erlotinib RNA-seq signature across two independent public datasets.

  7. Interaction network

    planned

    the STRING neighbourhood and pathway membership at two confidence thresholds.

  8. Phylogenetics

    planned

    conservation of EGFR orthologs across vertebrates and selection analysis.

  9. Drug binding

    planned

    erlotinib versus osimertinib binding, and how T790M and C797S explain resistance, from co-crystal structures.

  10. CPTAC stratification

    planned

    proteomic and phosphoproteomic comparison of EGFR-mutant and wild-type lung adenocarcinoma.

  11. Manuscript

    planned

    assembly and bioRxiv submission.

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