Evidence map›Paper›PMID 40667078›Full record

ArticlebioRxiv : the preprint server for biology2025

Genome-wide rules of transcription factor cooperativity revealed through

Xuening He, Hjörleifur Einarsson, Petra Páleníková, Sarah Rennie, Dewei Hu, Ruining Cui, Christian Vaagensø, Kasper Lage, Robert Krautz, Robin Andersson

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors.

Xuening HeSection for Computational and RNA Biology, Department of Biology, University of Copenhagen, Denmark.ORCID 0000-0001-5787-5076
Hjörleifur EinarssonSection for Computational and RNA Biology, Department of Biology, University of Copenhagen, Denmark.ORCID 0000-0002-0565-9053
Petra PáleníkováThe Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, USA.
Sarah RennieSection for Computational and RNA Biology, Department of Biology, University of Copenhagen, Denmark.ORCID 0000-0001-9731-6957
Dewei HuNovo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark.ORCID 0009-0005-5823-1498
Ruining CuiSection for Computational and RNA Biology, Department of Biology, University of Copenhagen, Denmark.ORCID 0009-0008-0499-9348
Christian VaagensøSection for Computational and RNA Biology, Department of Biology, University of Copenhagen, Denmark.
Kasper LageThe Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, USA.ORCID 0000-0001-6827-6239
Robert KrautzSection for Computational and RNA Biology, Department of Biology, University of Copenhagen, Denmark.ORCID 0000-0003-0457-1348
Robin AnderssonSection for Computational and RNA Biology, Department of Biology, University of Copenhagen, Denmark.ORCID 0000-0003-1516-879X

Funding

2/3 Building Integrative CNS Networks for Genomic Analysis of AutismR01MH109903 · NIMH · MASSACHUSETTS GENERAL HOSPITAL · PI HANSEN, KASPER LAGE · 2016 to 2020
$1.4M
From genetic risk variants to convergent protein networks: an integrative approach to elucidate the causal molecular mechanisms of schizophrenia.U01MH121499 · NIMH · BROAD INSTITUTE, INC. · PI HANSEN, KASPER LAGE · 2020 to 2020
$829k
NIMH NIH HHS R01 MH109903NIMH NIH HHS U01 MH121499
6 · The paper itself

Abstract

Transcription factor (TF) cooperativity plays a critical role in gene regulation. However, the underlying genomic rules remain unclear, calling for scalable methods to characterize the TF binding site (motif) syntax of regulatory elements. Here, we introduce DeepCompARE, a lightweight model paired with an

Identifiers

PMID40667078
PMCPMC12262439

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.