Read all 76 archived CBX3 and BRCA1 tracks at the KMT2A exon-11 anchor at SIGNAL level against a CTCF-anchor-matched null, and score the anchor's rank among its own class in each - no wet work, no new data, and it decides whether the sub-IDR peak is a foothold or a threshold artefact
also called the 76-track signal-level re-read · class-matched percentile of the KMT2A exon-11 anchor
Three public datasets show a faint signal for two repair proteins at one small spot in the KMT2A gene, faint enough that the standard filter throws it away. This is the computer-only experiment that would decide whether that faint signal is real, by reading all seventy-six available datasets and comparing the spot to thousands of similar spots in the same cells.
The same thing, for a scientist
**The question this settles.** `ana-q37-the-kmt2a-exon-11-anchor-carries-a-cbx3-and-a-brca1-peak-that-idr-removes` found a called peak on the exon-11 CTCF element in 3 of 180 archived tracks and, in ENCODE's own pre-IDR files, in 2 of 2 replicates of two experiments at global IDR 0.227 and 0.0588. That is a peak-level observation at one threshold. **It does not say whether the element carries a reproducible signal-level enrichment relative to the class it belongs to**, which is the only question a CTCF anchor can be asked honestly (`concept-a-genome-wide-null-flatters-any-interval-that-belongs-to-an-enriched-class`). **Design.** 45 CBX3 and 31 BRCA1 hg38 tracks exist across ChIP-Atlas and ENCODE. For each, read the mean signal over the seven Q35 intervals and over **N = 2,000 CTCF anchors of the same cell type**, drawn from that cell type's own CTCF peak set, matched on peak width and on distance to the nearest TSS. Report the exon-11 anchor's **percentile rank among its own class**, per track, not its fold over a genome-wide tile median - the failure Q35 itself identified, where the *KMT2A* promoter fell from the top 0.07% of 1.51 M tiles to 1.24x against housekeeping controls. **Statistic and pre-declared decision rule.** The anchor **fires** if its class-matched percentile is **above the 75th percentile of same-cell-type CTCF anchors in at least 60% of interpretable tracks of one protein**, and the same statistic computed at the 6 non-anchor Q35 intervals stays below the 50th. It **fails** if the median percentile across interpretable tracks is between the 25th and 75th - i.e. the anchor is an ordinary CTCF anchor for that protein. **What makes this cheap and what makes it fail.** Every input is a public bigWig. There is no antibody, no cell culture and no consent question. The practical constraints are recorded because this project has been burned by all of them: **bin size must be measured per file before any 147 bp number is quoted**; **the build must be read from each FILE's own chrom table across at least five chromosomes**, because padding is a property of files and not of series; **Content-Length and md5 must be compared before two accessions are counted as two replicates**; and **pybigtools 0.3.0 returns NaN for uncovered bases**, so every interval is read twice, once with `fillna` for the honest coverage fraction and once with `nan_to_num` for the statistic. Disk is the real constraint - the CBX3 LP-1 track alone is 467 MB and the DNA2 HCT116 track 585 MB - so the loop must download, analyse and delete one file at a time. **Why it is worth doing even though the likely answer is negative.** Q35's own class-matched read put the element at 0.34-1.25x against 6,000 CTCF anchors, and this beat's peak-level class-matched read found 30.2% of K562 CTCF anchors carry a CBX3 peak. **Both point to 'ordinary anchor'.** The value is that the corpus currently holds two contradictory headline sentences - *no occupancy above background* and *a peak at the element in three tracks* - and a class-matched signal-level number over 76 tracks replaces both with one that can be quoted.
| design | For each of 45 CBX3 and 31 BRCA1 human hg38 tracks (ChIP-Atlas eachData/bw plus ENCODE fold-change-over-control bigWigs), compute the mean signal over the seven Q35 KMT2A intervals and over 2,000 CTCF anchors of the same cell type matched on peak width and TSS distance; report the exon-11 anchor's percentile rank within that class-matched distribution, per track. |
|---|---|
| readout | per-track class-matched percentile of the exon-11 CTCF element (chr11:118,488,614-118,488,760) and of the 1,048 bp ctcf_element (chr11:118,488,159-118,489,206); secondary readout is the same percentile at the six non-anchor intervals |
| controls | C1 per-track dynamic-range gate - mean signal over the track's own top 500 peaks must be >= 5x the genome-wide same-width tile median, else the track is excluded as uninterpretable and reported as excluded. C2 positive - housekeeping promoters (ACTB, GAPDH, RPLP0, EEF1A1, TSS +/- 1 kb from live Ensembl GRCh38) for BRCA1, and the chr19q13 KRAB-ZNF cluster gene bodies for CBX3. C3 negative - the largest Ensembl-gene-free interval on chr2, fetched live. C4 instrument - a CTCF track of the same cell type must place the exon-11 anchor above its own 90th percentile, or the pipeline cannot see this element in that cell. |
| cost tier | low |
| timeline | one to two days of compute, no wet work, no new data generation |
| what it cannot do | It cannot answer the damage-state question, which is what the mechanism actually predicts, and it cannot reach a KMT2A-rearranged or fetal progenitor cell, because no CBX3 or BRCA1 track exists in one. A negative here bounds the resting state in twelve cell types and nothing more. |
| prior expectation recorded before running | NEGATIVE. Q35's class-matched read put the element at 0.34-1.25x against 6,000 CTCF anchors, and this beat's peak-level class-matched read found 30.2% of K562 CTCF anchors carry a CBX3 peak. The value of running it is a single quotable number in place of two contradictory sentences, not a new positive. |
practical constraints that have broken this project before
[ "measure the MODAL run length of raw intervals across the KMT2A span per file before quoting any number for a 147 bp interval; if the modal bin exceeds the interval width, report 'one bin, not a measurement'", "read the build from each FILE's own chrom table across chr1, chr2, chr11, chr19 and chrX - padding is a property of individual files, and a nearest-build test on chr11 alone picks the wrong build for at least one file in this project's history", "HTTP HEAD Content-Length and compare md5 before counting two accessions as two replicates - one deposited file under two accessions understates every standard error by root 2", "pybigtools 0.3.0 returns NaN for uncovered bases where 0.2.x filled 0; pass fillna and nan_to_num explicitly, and read every interval twice (once for covered_fraction, once for the statistic)", "summary= is ignored unless bins= is set; pass bins=1 explicitly", "C: has roughly 20 GB free, not the 85 GB the environment notes claim; download, analyse and delete one file at a time - the CBX3 LP-1 bigWig is 467 MB and the DNA2 HCT116 bigWig 585 MB" ]
inputs
{
"CBX3_tracks": 45,
"BRCA1_tracks": 31,
"source": "ChIP-Atlas https://chip-atlas.dbcls.jp/data/hg38/eachData/bw/<SRX>.bw plus the ENCODE fold-change-over-control bigWigs already selected in analyses/q35-brca1-cbx3-encode-at-the-kmt2a-locus/q35_selected.json",
"anchor_sets": "ENCODE optimal IDR CTCF peak sets per cell type where one exists (K562 ENCFF843VHC 44,722 anchors; HeLa-S3 ENCFF154APE 41,050), otherwise the deepest ChIP-Atlas CTCF track of that cell type"
}decision rule written before any signal is read
{
"FIRES": "the exon-11 anchor sits above the 75th percentile of same-cell-type CTCF anchors in >= 60% of interpretable tracks of one protein, while the six non-anchor intervals stay below the 50th",
"FAILS": "the median class-matched percentile across interpretable tracks lies between the 25th and the 75th - the anchor is an ordinary CTCF anchor for that protein",
"UNINTERPRETABLE": "fewer than 10 tracks of that protein pass the C1 gate, or C4 fails in the cell type of interest"
}- If this returns a clean negative it will be used to close the question, and it can only close the RESTING state in twelve non-leukaemic cell types. The damage-state question and the KMT2A-rearranged cell type would still be untouched, and the entry that quotes the negative must say so or it repeats exactly the error this beat found in cycle 63.
- If it returns a positive, the immediate temptation is a menin-inhibitor-plus-repair-inhibitor combination argument, and that argument would rest on a resting-state occupancy percentile in HeLa and K562 - neither of which is a KMT2A-rearranged blood cell.
- Should the same re-read cover CBX5 (29 tracks) and CBX1 (8 tracks) in the same run? The marginal cost is small and the HP1 paralogues are the family this graph cannot separate by name, accession length or literature.
- Is there any CBX3 or BRCA1 track in a KMT2A-rearranged line anywhere? The census says no across three archives, which means this experiment can never answer the question in the cell type that matters and a CUT&RUN in SEM or RS4;11 is the only route.
- What class base rate would make a positive uninterpretable? If CBX3 occupies 67% of CTCF anchors in some cell types, as it does in HCT116, then a high percentile at one anchor carries almost no information there, and the design should probably exclude tracks above some class base rate rather than reporting them.
- E1established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
The inputs exist and are public: 45 distinct CBX3 and 31 distinct BRCA1 human ChIP-seq SRX are indexed in ChIP-Atlas with hg38 bigWig and peak files served directly, spanning 8 and 12 cell types respectively, and the ENCODE fold-change-over-control bigWigs for the 13 experiments Q35 read are already selected and md5-recorded in this repository.
ChIP-Atlas 2025 update: 10-year anniversary of a data-mining platform for exploring epigenomic landscape. · Zou Z, Ohta T, Kasukawa T, et al. · Nucleic Acids Research 2026What this evidence cannot show
ChIP-Atlas bigWigs are read-depth coverage, not fold change over an input control, so they are not directly comparable to the ENCODE fold-change tracks and the two families must be percentile-ranked separately rather than pooled. Track depth varies by more than an order of magnitude across the 76, which is why the C1 dynamic-range gate is mandatory rather than advisory.
Evidence that argues against this (1)
- Two of six CTCF positive controls in this beat's peak-level sweep failed on depth alone, which means the C4 instrument control will also fail in some cell types and the effective n will be smaller than 76. An experiment whose control fails in an unknown fraction of its inputs cannot state its power in advance, and this one does not. Q37-archive-sweep 2026
- E2strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.dataset
The class-matched null is the right null for this element and the genome-wide null is not, because the element is itself a strong CTCF anchor: Q35 measured the KMT2A promoter falling from the top 0.07% of 1.51 million genome-wide tiles to 1.24x against its own housekeeping controls, and the exon-11 element from an apparent enrichment to 0.34-1.25x against 6,000 CTCF anchors of the same cell type.
concept-a-genome-wide-null-flatters-any-interval-that-belongs-to-an-enriched-class · Q35-encode-reanalysis · this graph 2026What this evidence cannot show
Matching on peak width and TSS distance does not match on copy number, replication timing or local mappability, any of which can shift a single anchor's apparent signal. The 2,000-anchor sample size is chosen for compute rather than from a power calculation.
Evidence that argues against this (1)
- A class-matched null can be too strict: if CBX3 genuinely coats CTCF anchors as part of the mechanism this graph proposes, then asking whether the KMT2A anchor is unusual AMONG CTCF anchors is asking the wrong question, and a negative would be recorded as 'HP1-gamma is not at KMT2A' when the true finding is 'HP1-gamma is at all CTCF anchors including this one'. The design mitigates this only by reporting the class base rate alongside the percentile. Q37-archive-sweep 2026
runs control C4 of that pre-registration for the first time; it fails in 6 of 6 cell types because the premise that this is a top-decile CTCF anchor is false
the complete 124-file pre-IDR census is the measurement the pre-registered experiment specified, run at peak level across all 13 experiments
the run of the pre-registered signal-level re-read, reporting against the prior that was recorded before any data was read
the no-wet-work class-matched signal-level read that scores falsifiers one and two
45 archived CBX3 tracks at the exon-11 anchor against a class-matched CTCF-anchor null
31 archived BRCA1 tracks; BRCA1 is the discriminating protein because its class base rate is 10.3%
the design's null is class-matched for exactly this reason