Evidence map›Paper›PMID 40791531›Full record

ArticlebioRxiv : the preprint server for biology2025

Expanding the DNA Motif Lexicon of the Transcriptional Regulatory Code.

Jingyu Fan, Virendra K Chaudhri, Deepa Bisht, Nicholas A Pease, David Reed Hall, Peter Gerges, Vivian Fang Yi, Susan Kales, Ching-Huang Ho, Jishnu Das and 5 more

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

15 authors.

Jingyu FanCenter for Systems Immunology and the Departments of Immunology and Computational and Systems Biology, University of Pittsburgh, PA, USA.ORCID 0000-0003-2440-2015
Virendra K ChaudhriCenter for Systems Immunology and the Departments of Immunology and Computational and Systems Biology, University of Pittsburgh, PA, USA.
Deepa BishtDepartment of Epigenetics and Molecular Carcinogenesis, Department of Bioinformatics and Computational Biology, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA.
Nicholas A PeaseCenter for Systems Immunology and the Departments of Immunology and Computational and Systems Biology, University of Pittsburgh, PA, USA.
David Reed HallCenter for Systems Immunology and the Departments of Immunology and Computational and Systems Biology, University of Pittsburgh, PA, USA.
Peter GergesCenter for Systems Immunology and the Departments of Immunology and Computational and Systems Biology, University of Pittsburgh, PA, USA.
Vivian Fang YiCenter for Systems Immunology and the Departments of Immunology and Computational and Systems Biology, University of Pittsburgh, PA, USA.
Susan KalesThe Jackson Laboratory, Bar Harbor, ME, USA.
Ching-Huang HoCenter for Systems Immunology, Benaroya Research Institute, Seattle, WA, USA.
Jishnu DasCenter for Systems Immunology and the Departments of Immunology and Computational and Systems Biology, University of Pittsburgh, PA, USA.
John P RayCenter for Systems Immunology, Benaroya Research Institute, Seattle, WA, USA.
Ryan TewheyThe Jackson Laboratory, Bar Harbor, ME, USA.
Clifford A MeyerDepartment of Data Sciences, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA, USA.
Nidhi SahniDepartment of Epigenetics and Molecular Carcinogenesis, Department of Bioinformatics and Computational Biology, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA.
Harinder SinghCenter for Systems Immunology and the Departments of Immunology and Computational and Systems Biology, University of Pittsburgh, PA, USA.ORCID 0000-0002-6330-8526

Funding

Linking genome variation to transcriptional network dynamics in human B cellsU01HG012041 · NHGRI · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI Jishnu Das, HARINDER SINGH · 2021 to 2026
$6.1M
A generalizable framework for linking single-cell genomic states with cell fate outcomes in hematopoiesisRC2DK122376 · NIDDK · CINCINNATI CHILDRENS HOSP MED CTR · PI GRIMES, H. LEIGHTON · 2020 to 2024
$5.3M
High-Throughput Computing for Genomics and Bioinformatics ResearchS10OD028483 · OD · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI LEE, ADRIAN V · 2021 to 2021
$574k
NHGRI NIH HHS U01 HG012041NIDDK NIH HHS RC2 DK122376NIH HHS S10 OD028483
6 · The paper itself

Abstract

Transcriptional regulatory sequences in metazoans contain intricate combinations of transcription factor (TF) motifs. Stereospecific arrangements of simple motifs constitute composite elements (CEs) that enhance DNA-protein interaction specificity and enable combinatorial regulatory logic. Despite their importance, CEs remain underexplored. We advance CE discovery and functional characterization by developing an integrated framework that combines computational prediction, experimental testing and deep learning. The extended TF motif catalog comprises both synergistic and counteracting CEs, which are supported by evidence of TF binding

Indexed as

composite elementsdeep learninggene regulatory lexiconTF motifs

Identifiers

PMID40791531
PMCPMC12338572

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
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.