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Genomic Claims You Can Trace

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     Long Analysis Plan


    KRAS mutation hotspots & co-mutations (from paper Table 1: CRC MSS vs MSI)
    Graphs below use only the numeric values explicitly provided in the supplied research data for KRAS MSS/MSI frequencies, codon frequencies, and a subset of MSS KRAS co-mutations.
    Important limitation: the provided dataset does not include the full “KRAS mutation hotspots” residue/position table, nor the full cBioPortal co-mutation matrix for TCGA. Therefore, the visuals are faithful to what’s provided, not a complete TCGA cBioPortal reconstruction.
    Codons shown include the set listed in the supplied research data (G12D, G12V, G13D, G12C, G12A, G12S), but only G12D/G12V/G12C have explicit MSS/MSI codon frequencies in the provided excerpt; remaining bars are left empty by construction (no extrapolation).
    The supplied research data provides only a subset of co-mutation gene names for MSS KRAS (APC, PIK3CA, FBXW7, AMER1, SMAD2) without co-mutation frequencies/odds ratios in the excerpt; therefore this figure is a label-only visualization and intentionally avoids pretending to quantify effect sizes.
    Skew, uncertainty, and what’s missing vs your request
    • “Hotspots”: The excerpt does not include residue/position-level hotspot counts for KRAS; it includes codon categories (e.g., G12D/G12V/G12C) instead. So the plots show codon frequencies, not amino-acid hotspot positions.
    • “TCGA cBioPortal”: The provided numeric values are summarized from the paper’s compiled analyses; the excerpt does not provide a TCGA-specific cBioPortal export table to recreate the full mutation hotspot heatmaps or co-mutation matrix.
    • Co-mutations: Only MSS KRAS co-mutation gene names (subset) and one MSI-associated item (APC, plus BRAF as “low mutual exclusivity”) are present in the excerpt; effect sizes are missing.
    • Potential selection bias: The paper excerpt notes heterogeneity across cohorts and sequencing platforms and possible cohort composition effects; this can impact observed frequencies and co-mutation patterns.
    Note on citation rigor: the numeric values plotted here are taken only from the supplied research-data excerpt for the paper . Without the complete Table 1 rows (and/or a TCGA cBioPortal export), the requested hotspot+co-mutation matrix cannot be fully reconstructed.


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    Updated: April 14, 2026

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    Extract Table 1 KRAS hotspot and co-mutation fields, compute MSS/MSI contrasts, then render hotspot heatmaps and co-mutation networks using the provided frequencies and contingency statistics.



     Science Art


    Create Graphs: KRAS mutation hotspots and co-mutations (TCGA cBioPortal) from the paper’s Table 1 Science Art

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