Evidence map›Paper›PMID 39763964›Full record

ArticlebioRxiv : the preprint server for biology2024

A new pipeline SPICE identifies novel JUN-IKZF1 composite elements.

Peng Li, Sree H Pulugulla, Sonali Das, Jangsuk Oh, Rosanne Spolski, Jian-Xin Lin, Warren J Leonard

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. 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

5 · Who and what money

Authors and funding

7 authors.

Peng LiLaboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892.
Sree H PulugullaLaboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892.
Sonali DasLaboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892.
Jangsuk OhLaboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892.
Rosanne SpolskiLaboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892.
Jian-Xin LinLaboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892.
Warren J LeonardLaboratory of Molecular Immunology, Immunology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Transcription factor partners can cooperatively bind to DNA composite elements to augment gene transcription. Here, we report a novel protein-DNA binding screening pipeline, termed Spacing Preference Identification of Composite Elements (SPICE), that can systematically predict protein binding partners and DNA motif spacing preferences. Using SPICE, we successfully identified known composite elements, such as AP1-IRF composite elements (AICEs) and STAT5 tetramers, and also uncovered several novel binding partners, including JUN-IKZF1 composite elements. One such novel interaction was identified at CNS9, an upstream conserved noncoding region in the human

Identifiers

PMID39763964
PMCPMC11703198

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Registered trials

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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.