Evidence map›Paper›PMID 39786853›Full record

ArticleeLife2025

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

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

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in eLife, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

7 authors.

Peng Li *Amgen Inc, Rockville, United States.ORCID https://orcid.org/0000-0002-4721-5936
Sree Pulugulla *Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, NIH, Bethesda, United States.
Sonali DasLaboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, NIH, Bethesda, United States.
Jangsuk OhLaboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, NIH, Bethesda, United States.
Rosanne SpolskiLaboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, NIH, Bethesda, United States.
Jian-Xin LinLaboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, NIH, Bethesda, United States.
Warren J LeonardLaboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, NIH, Bethesda, United States.ORCID https://orcid.org/0000-0002-5740-7448

Funding

Intramural NIH HHS Z99 HL999999NHLBI NIH HHS Z99 HL999999
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

Indexed as

Ikaros Transcription FactorProtein BindingBinding SitesB-LymphocytesHumansT-LymphocytesTranscription Factor AP-1Ikaros Transcription FactorTranscription Factor AP-1AP1computational biologyIKZF1IL-10IL-21immunologyinflammationJUNmouseProtein-DNASPICEsystems biology

Identifiers

PMID39786853
PMCPMC11717359

What OpenQuestion holds

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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.