Evidence map›Paper›PMID 42523385›Full record

ArticlebioRxiv : the preprint server for biology2026

Reference Regulatory Element-Guided Gene Expression Analysis for Mechanistic Inference of Gene Regulatory Networks.

Lixin Ren, Ishita Debnath, Zhana Duren

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 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

3 authors.

Lixin RenCenter for Computational Biology and Bioinformatics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
Ishita DebnathCenter for Computational Biology and Bioinformatics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
Zhana DurenCenter for Computational Biology and Bioinformatics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA.ORCID 0000-0003-4685-811X

Funding

Statistical methods for interpretation of genetic variants by gene regulatory networksR35GM150513 · NIGMS · INDIANA UNIVERSITY INDIANAPOLIS · PI Zhana Duren · 2023 to 2026
$1.4M
Statistical methods for gene regulatory analysis of substance use disorderR21DA060503 · NIDA · INDIANA UNIVERSITY INDIANAPOLIS · PI DUREN, ZHANA · 2024 to 2025
$426k
NIDA NIH HHS R21 DA060503NIGMS NIH HHS R35 GM150513
6 · The paper itself

Abstract

Regulatory genomics faces a depth-breadth gap: deep multi-omics provides regulatory detail but is difficult to scale, whereas broad expression datasets often lack the regulatory structure needed for mechanistic Gene Regulatory Network (GRN) analysis. We developed Regulatory Elements Guided Analysis (REGA), an interpretable framework that uses reference Regulatory Element (RE) catalogs to infer transcription factor (TF)-RE-gene programs from gene expression data. Across ChIP-seq, knockdown, Hi-C,

Identifiers

PMID42523385
PMCPMC13405040

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.