None of the five selective unwritten interactors survives a null, and FANCD2 - the one that carried a story - is the second weakest of them at p = 0.12
also called permutation null on the triage shortlist · FANCD2 selectivity does not hold
Yesterday we found five proteins that looked more needed by this cancer than by other leukaemias, and built two write-ups on them. Testing whether those differences could have arisen by chance: none of them holds up once you account for having looked at 254 proteins to find five.
The same thing, for a scientist
`ana-five-unwritten-interactors-that-are-also-selective-dependencies` said in its own caveats *"No permutation null was computed; this is a triage, not a test."* This computes it, with 50,000 label permutations per gene and the within-set rank as a second null. | gene | difference | perm p | rank in 254 | Bonferroni over 254 | |---|---:|---:|---:|---:| | DAXX | -0.305 | **0.0128** | 4 (1.6%) | 3.25 | | TRAF2 | -0.181 | 0.1618 | 18 (7.1%) | >1 | | HDGFL2 | -0.161 | **0.0187** | 18 (7.1%) | 4.75 | | QKI | -0.157 | **0.0060** | 19 (7.5%) | 1.52 | | **FANCD2** | -0.153 | **0.1241** | 22 (8.7%) | >1 | **Nothing survives correction over the 254 the shortlist was drawn from**, and two of the five - TRAF2 and **FANCD2** - are not significant even uncorrected. **FANCD2 is the one that matters, because it was carrying a story.** A convergence was written up between a 2003 paper titled *Menin associates with FANCD2*, this graph's unexplained Fanconi selectivity signal, and this DepMap difference. **The DepMap leg is gone.** Whatever survives has to survive on the literature alone.
Why the shortlist was an artefact of its own threshold
The triage-set difference distribution over 254 genes: min -0.527, Q1 -0.046, median -0.006, Q3 +0.039, max +0.262.
The shortlist was defined as difference at or below -0.15 with pan-essentiality above -0.5. Twenty-two of the 254 clear the difference bar; the pan-essentiality filter cut that to five. So the headline number - five of 254 - is mostly the second filter doing work, and the first filter selects a populated tail rather than an outlier.
This is the failure the project keeps meeting from a new angle. A similarity or consistency score finds candidates and reading separates defect from design; here a selectivity score found candidates and only a null separates signal from tail. Four instruments in four cycles flagged more than was wrong. This is the fifth, and it flagged five things of which at best one is real.
QKI has the best p-value and the smallest claim. Its index mean is -0.122 against +0.035 in other leukaemia lines - it is close to not required at all in the comparator - so the difference is clean and the effect is negligible. A low p on a negligible effect is exactly what a large enough comparator arm buys.
What this does to the two entries written on the shortlist
gene-daxx survives as an entry and its evidence item is downgraded. DAXX is still rank 4 of 254 with p = 0.0128, the strongest of the five - and it still does not survive correction, and the entry already said the honest prior is artefact and that it was written so a future cycle could kill it cheaply. It has now been partly killed by the cycle that wrote it, which is the outcome that entry was shaped for. The literature absence it records - zero papers connecting DAXX to this disease - is unaffected, because that was never a dependency claim.
gene-hdgfl2 is unaffected in substance. Its DepMap evidence was already graded moderate and already contradicted by the paper that measured it directly: HRP-2 knockdown reduces colony formation in MLL-germline lines as much as in MLL-rearranged ones. The null agrees with the colony assay. Two independent instruments now say the same thing, and the entry's reason for existing - menin selecting between two IBD paralogues - never rested on selectivity at all.
The FANCD2 convergence loses a leg and should be stated as two legs, not three. The 2003 association paper and the unexplained Fanconi complex signal remain; the dependency number does not. I had sent that number to the menin-interactome agent as context, flagged as weak - it is weaker than flagged, and the correction has been sent.
What a null cannot fix, and why that matters more than the p-values
Every number here rests on eleven KMT2A-rearranged cell lines. This project has already established what those eleven are: nine individuals, of whom the index-fusion arm is three people - a 32-year-old, a 10-year-old and one 5-year-old counted twice - and none is under one year. The lymphoid half of the arm is four lines. And at least ten infant-derived KMT2A::AFF1 lines exist, none of them screened, including one from a nine-day-old.
So a permutation test here answers 'could this allocation of eleven adult and paediatric lines produce this split by chance' and nothing more. It does not make the panel the disease. The right conclusion from this analysis is not that these five genes are uninteresting - it is that a screen with no infant index-fusion line cannot settle a question about infant index-fusion biology, and the correct next move is the screening gap rather than a better statistic on the same eleven lines.
ALL-PO (CVCL_1069, age 4 months) is already a DepMap collection line with methylation, exome, proteomics and RNA-seq and no CRISPR gene-effect value. One screen in a line already in hand.
- Recompute with a permutation-based FDR rather than Bonferroni over 254, and report both. The genes are not independent and Bonferroni is the harshest defensible choice.
- Power the design honestly: with 11 index lines against 43, what effect size would this test detect at 80% power? If the answer is larger than any difference in the set, the null is measuring the panel and not the genes.
- Screen ALL-PO (CVCL_1069, age 4 months), which is already a DepMap collection line with no CRISPR gene-effect value. No statistic on the current eleven lines substitutes for one infant index-fusion line.
- Apply the same null retrospectively to the other DepMap-derived shortlists in this graph. This one was tested because its own entry admitted the gap; the others have not been.
- E1established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.analysis
Under 50,000 two-sided label permutations per gene, the five-gene shortlist gives DAXX p = 0.0128, HDGFL2 p = 0.0187, QKI p = 0.0060, FANCD2 p = 0.1241 and TRAF2 p = 0.1618. Bonferroni correction over the 254 genes the shortlist was drawn from leaves none below 0.05. Within the triage set the five rank 4th, 18th, 18th, 19th and 22nd of 254, and 22 of the 254 meet the shortlist's own difference threshold.
Label-permutation and within-set nulls for the five-gene shortlist of unwritten interactors that are also selective dependencies · Oncofusion knowledge graph (internal analysis) 2026What this evidence cannot show
Run 2026-09-20 with seed 20260920. Established as a fact about the computation. **Bonferroni over 254 is the conservative choice and is arguable** - the 254 are not independent tests, since curated interactors of one complex share biology and cell lines are shared across every gene, so a permutation-based FDR would be less harsh. It is used because the alternative error - selecting 5 from 254 and then correcting for 5 - is the one this analysis exists to avoid. **The null tests allocation, not biology**: it asks whether these eleven lines could fall this way by chance, not whether the gene matters in this disease.
Evidence that argues against this (1)
- A null that kills everything is as suspect as one that kills nothing. With 11 index lines against 43, the smallest achievable two-sided permutation p is bounded well above zero for many allocations, so this design has limited power by construction and a true effect of modest size would fail it. Reading 'none survives' as 'none is real' would be the mirror of the error being corrected. Oncofusion knowledge graph (internal analysis) 2026
- E2established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
FANCD2's selectivity difference of -0.153 between KMT2A-rearranged and other leukaemia lines has a two-sided permutation p of 0.1241 and is not significant even before correction for multiple testing, making it the second weakest member of the shortlist it was drawn from.
DepMap CRISPR (Chronos) gene effect via Open Targets GraphQL, 11 KMT2A-rearranged against 43 other leukaemia lines · Broad Institute DepMap via Open Targets 2026What this evidence cannot show
Computed 2026-09-20 from the same Open Targets query as the triage. **This removes a leg from a three-part convergence and does not touch the other two**: the 2003 paper reporting that menin associates with FANCD2 stands as a published association, and this graph's Fanconi complex selectivity signal - 2nd of 719 complexes - was measured by a different analysis on a different unit and is unaffected by this gene-level null.
Evidence that argues against this (1)
- The complex-level Fanconi signal survives while the gene-level FANCD2 signal does not, and those are consistent rather than contradictory - a set of genes can shift together in a way no single member does alone, which is the entire argument for complex-level testing. This result therefore argues for keeping the Fanconi question open at the complex level and dropping it at the FANCD2 level. Jin S et al. 2003
- E3strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.journal-article
The permutation result for HDGFL2 agrees with the direct experiment: the gene does not show a KMT2A-rearranged-specific requirement, matching the published finding that HRP-2 knockdown reduces colony formation in MLL-germline lines K562, Kasumi-1 and Nalm-6 as much as in the MLL-rearranged lines THP-1 and SEM.
Unlike Its Paralog LEDGF/p75, HRP-2 Is Dispensable for MLL-R Leukemogenesis but Important for Leukemic Cell Survival · Cells 2021What this evidence cannot show
The agreement is between a null that fails to reject and an experiment that shows a non-specific effect, which are not the same kind of statement - **failing to find selectivity is weaker than showing non-selectivity**, and only the colony assay does the latter. Graded `strong` as a generalisation across two instruments rather than `established`.
Evidence that argues against this (1)
- Two instruments agreeing is worth less when one of them was built by this project and tuned by this project. The colony assay is the independent evidence; the permutation test is a check on our own arithmetic. Oncofusion knowledge graph (internal analysis) 2026
none of its five survives a null it did not compute
its dependency item, which the entry invited
agrees with the colony data already in that entry
the complex-level signal survives; the FANCD2 gene-level leg does not
- related to →Pan-essentiality: checked for all eight, and cleared — but a shallow dependency is its own problem
the filter that cut 22 candidates to five
the rule this tool makes cheap to follow
QKI's DepMap selectivity claim died in that null; the patient-cohort tumour-suppressor evidence in this entry is independent of it and must not inherit its credibility