{
  "record_type": "Published-method transcription; incomplete reproduction record",
  "source_page": "https://ugurcemyildiz.me/research/cancer-bioinformatics/",
  "sources": [
    "TCGA Pan-Cancer Atlas",
    "GTEx"
  ],
  "analyses": [
    {
      "platform": "GEPIA2",
      "cohorts": [
        "BRCA",
        "LUAD",
        "COAD"
      ],
      "method": "One-way ANOVA",
      "reported_thresholds": {
        "log2_fold_change": 1,
        "p_value": 0.01
      }
    },
    {
      "platform": "cBioPortal",
      "cohorts": [
        "breast",
        "lung",
        "colorectal"
      ],
      "method": "Copy-number state, mutations and mRNA expression"
    },
    {
      "platform": "Kaplan–Meier Plotter",
      "cohorts": [
        "BRCA",
        "LUAD",
        "READ"
      ],
      "endpoint": "Overall survival",
      "threshold_selection": "Automatic",
      "reported_luad_p_value": 0.007
    },
    {
      "platform": "TIMER2.0",
      "method": "Spearman correlation between CXCR4 expression and inferred CD8+ T-cell infiltration"
    },
    {
      "platform": "STRING",
      "method": "Predicted functional association network"
    }
  ],
  "expression_figure": {
    "path": "/images/cancer-bioinformatics/gepia2-cxcr4-expression.jpg",
    "sample_counts_read_from_labels": {
      "BRCA": {
        "tumour": 1085,
        "normal": 291
      },
      "LUAD": {
        "tumour": 483,
        "normal": 347
      },
      "COAD": {
        "tumour": 275,
        "normal": 349
      }
    },
    "note": "Counts transcribed from the published figure, not independently downloaded or verified against a dataset version."
  },
  "available_survival_figure": {
    "path": "/images/cancer-bioinformatics/kaplan-meier-survival-curves.png",
    "cohort": null,
    "displayed_hr": 1.39,
    "displayed_95_percent_ci": [
      0.62,
      3.09
    ],
    "displayed_log_rank_p_value": 0.42,
    "note": "A single unlabelled-cohort plot; it does not visually verify the reported LUAD p = 0.007 result."
  },
  "unavailable": [
    "analysis_dates",
    "dataset_versions",
    "survival_cohort_sizes",
    "numerical_expression_cutoffs",
    "luad_hazard_ratio",
    "luad_confidence_interval",
    "algorithm_specific_correlations",
    "original_cohort_specific_survival_exports",
    "exported_input_data"
  ],
  "interpretation": "Observational associations do not establish causality; the automatic survival threshold needs independent validation."
}