Evidence map›Paper›PMID 41518507›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2026

Web-Based Discovery of Regulatory Motifs in Non-model Plants.

Najla Ksouri, Ammar Abdalrahem, Francesc Montardit-Tarda, Jaime A Castro-Mondragón, Jacques van Helden, Yolanda Gogorcena, Bruno Contreras-Moreira

Abstract read
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In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2026. 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

7 authors.

Najla KsouriEstación Experimental de Aula Dei-CSIC, Zaragoza, Spain.
Ammar AbdalrahemEstación Experimental de Aula Dei-CSIC, Zaragoza, Spain.
Francesc Montardit-TardaEstación Experimental de Aula Dei-CSIC, Zaragoza, Spain.
Jaime A Castro-MondragónAix-Marseille Univ, INSERM UMR_S 1090, Theory and Approaches of Genome Complexity (TAGC), Marseille, France.
Jacques van HeldenAix-Marseille Univ, INSERM UMR_S 1090, Theory and Approaches of Genome Complexity (TAGC), Marseille, France.
Yolanda GogorcenaEstación Experimental de Aula Dei-CSIC, Zaragoza, Spain.
Bruno Contreras-MoreiraEstación Experimental de Aula Dei-CSIC, Zaragoza, Spain. bcontreras@eead.csic.es.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

This protocol describes step-by-step how to discover and annotate DNA motifs in regulatory regions of clusters/modules of co-expressed genes in plants, including non-model species. It also explains how to control the significance of the results and how to associate the discovered motifs with potentially binding transcription factors (TFs). These tasks can all be done in a web browser. While it uses the plant-dedicated mirror of the Regulatory Sequence Analysis Tools (RSAT, http://plants.rsat.eu ), it can be used on any organism hosted at any RSAT mirror.

Indexed as

Computational BiologyNucleotide MotifsPlantsRegulatory Sequences, Nucleic AcidGene Expression Regulation, PlantGenome, PlantInternetPromoter Regions, GeneticSequence Analysis, DNASoftwareTranscription FactorsWeb BrowserTranscription FactorsClusterDNA motif discoveryModuleNon-model speciesPlant genomeProximal promoter

Identifiers

PMID41518507

What OpenQuestion holds

Textmetadata
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.