RUN, with its positive control: knocking down KDM4B and KDM4C together raises H3K9me3 at the +1 nucleosome of 2,000 active promoters by 35.7 percentile points, moves the KMT2A promoter's +1 nucleosome by the same 35.3, and moves the 90 kb KMT2A gene body 5.05 points the WRONG way - so the methyl-poor domain is not an erasure product

[
  "analyses/q116-h3k9-axis-at-the-locus/results.json",
  "analyses/q116-h3k9-axis-at-the-locus/results_q2_eraser_arm.json",
  "analyses/q116-h3k9-axis-at-the-locus/results_q2_promoter_control.json"
]

{
  "shCTL": [
    "GSM4133820",
    "GSM4133821"
  ],
  "shKDM4B_shKDM4C": [
    "GSM4133822",
    "GSM4133823"
  ]
}

{
  "spearman_shCTL_vs_shCTL": 0.3247,
  "spearman_shKD_vs_shKD": 0.2592,
  "mean_spearman_across_condition": 0.2898,
  "preregistered_test": "within-condition rho must exceed across-condition rho",
  "result": "PASSES on the shCTL pair (0.3247 > 0.2898), FAILS on the shKD pair (0.2592 < 0.2898)",
  "verdict": "ARM INFORMATIVE - but on the strength of the genome-wide +1 nucleosome positive control, not on this test"
}

{
  "declared_before_reopening_the_tracks": true,
  "window": "TSS+1 to TSS+200 in the direction of transcription",
  "gene_sets": "2,000 highest-TPM protein-coding genes (ENCFF251DYL, TPM 63.74-10,242.87) versus 2,000 sampled from 5,644 with TPM < 0.1, seed 116",
  "shCTL_median_active_percentile": 21.725,
  "shKD_median_active_percentile": 57.431,
  "delta": 35.706,
  "per_replicate_shCTL": [
    43.45,
    0
  ],
  "per_replicate_shKD": [
    71.69,
    43.18
  ],
  "active_window_zero_fraction_per_track": [
    0.34,
    0.81,
    0.13,
    0.41
  ],
  "published_direction_reproduced": "PMID 34194047 Extended Data Fig. 7p",
  "same_comparison_at_the_1kb_promoter_window": -4.794,
  "reading": "the effect is confined to the +1 nucleosome, exactly where the paper places it"
}

{
  "shCTL_percentile_of_active_set": 0,
  "shKD_percentile_of_active_set": 35.25,
  "delta": 35.25,
  "reading": "moves like an average active promoter"
}

{
  "n_anchors": 56171,
  "median_abs_delta_percentile": 24.417,
  "p95_abs_delta_percentile": 60.358,
  "p99_abs_delta_percentile": 78.249,
  "frac_anchors_abs_delta_over_10": 0.5638,
  "frac_anchors_abs_delta_exceeding_own_replicate_spread": 0.0985,
  "frac_anchors_rising_in_KD": 0.491
}

{
  "exon11": {
    "shCTL": [
      0,
      0
    ],
    "shKD": [
      0,
      0
    ],
    "delta": 0,
    "verdict": "DOES NOT MOVE AT THE LOCUS"
  },
  "ctcf_element": {
    "shCTL": [
      31.45,
      0
    ],
    "shKD": [
      20.15,
      17.7
    ],
    "delta": 3.2,
    "verdict": "DOES NOT MOVE AT THE LOCUS"
  },
  "ctcf_summit_1kb": {
    "shCTL": [
      32.51,
      0
    ],
    "shKD": [
      21.15,
      18.57
    ],
    "delta": 3.61,
    "verdict": "DOES NOT MOVE AT THE LOCUS"
  },
  "dcal_cut_1kb": {
    "shCTL": [
      32.54,
      87.72
    ],
    "shKD": [
      0,
      0
    ],
    "delta": -60.13,
    "verdict": "MOVES AT THE LOCUS - RULE FIRED, VERDICT NOT CREDIBLE, within-control spread is 55.18 points (deviation D2)"
  },
  "bcr_core": {
    "shCTL": [
      63.61,
      61.69
    ],
    "shKD": [
      56.56,
      0.09
    ],
    "delta": -34.32,
    "verdict": "DOES NOT MOVE AT THE LOCUS"
  },
  "kmt2a_tss_2kb": {
    "shCTL": [
      77.17,
      0
    ],
    "shKD": [
      71.52,
      59.19
    ],
    "delta": 26.77,
    "verdict": "DOES NOT MOVE AT THE LOCUS"
  },
  "kmt2a_gene": {
    "shCTL": [
      7.6,
      7.7
    ],
    "shKD": [
      2.56,
      2.64
    ],
    "delta": -5.05,
    "within_shCTL_spread": 0.1,
    "within_shKD_spread": 0.08,
    "verdict": "DOES NOT MOVE AT THE LOCUS - below the 10-point threshold, though it exceeds both replicate spreads fiftyfold"
  }
}

{
  "shCTL": [
    18.18,
    20.26
  ],
  "shKD": [
    3.12,
    7.27
  ],
  "delta": -14.03,
  "note": "scored against N4, a null declared in section 6 for a DIFFERENT question; reported as secondary and not scored by the Q2 rule"
}