Evidence map›Paper›PMID 40432793›Full record

ArticleNAR genomics and bioinformatics2025

Inferring gene-pathway associations from consolidated transcriptome datasets: an interactive gene network explorer for

Michael A Bertagna, Lydia J Bright, Fei Ye, Yu-Yang Jiang, Debolina Sarkar, Ajay Pradhan, Santosh Kumar, Shan Gao, Aaron P Turkewitz, Lev M Z Tsypin

Abstract read
In one paragraph

Article in NAR genomics and bioinformatics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Molecular biology of the cell · 2026
    Article
  2. bioRxiv : the preprint server for biology · 2026
    Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

10 authors.

Michael A BertagnaDepartment of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, 60637, United States.ORCID https://orcid.org/0009-0009-4568-1608
Lydia J BrightDepartment of Biology, State University of New York at New Paltz, New Paltz, NY, 12561, United States.ORCID https://orcid.org/0000-0001-7185-9988
Fei YeMOE Key Laboratory of Evolution & Marine Biodiversity and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.ORCID https://orcid.org/0009-0002-7140-5833
Yu-Yang JiangDepartment of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, 60637, United States.ORCID https://orcid.org/0000-0002-0338-4252
Debolina SarkarNational Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University Campus, Pune, Maharashtra State, 411007, India.ORCID https://orcid.org/0009-0004-9731-4782
Ajay PradhanNational Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University Campus, Pune, Maharashtra State, 411007, India.ORCID https://orcid.org/0009-0004-7549-3978
Santosh KumarNational Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University Campus, Pune, Maharashtra State, 411007, India.ORCID https://orcid.org/0000-0002-9363-3530
Shan GaoMOE Key Laboratory of Evolution & Marine Biodiversity and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.ORCID https://orcid.org/0000-0003-2083-2616
Aaron P TurkewitzDepartment of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, 60637, United States.ORCID https://orcid.org/0000-0003-3531-5806
Lev M Z TsypinDepartment of Pathology, Stanford University School of Medicine, Palo Alto, CA, 94305, United States.ORCID https://orcid.org/0000-0002-0642-8468

Funding

PREDOCTORAL TRAINING IN GENETICS AND REGULATIONT32GM007197 · NIGMS · UNIVERSITY OF CHICAGO · PI ROTHMAN-DENES, LUCIA B. B · 1985 to 2020
$17.0M
Biogenesis of Dense Core Secretory Granules in TetrahymenaR01GM077607 · NIGMS · UNIVERSITY OF CHICAGO · PI TURKEWITZ, AARON P · 2006 to 2009
$1.1M
NIGMS NIH HHS R01 GM077607NIGMS NIH HHS T32 GM007197Wellcome Trust
6 · The paper itself

Abstract

Although an established model organism,

Indexed as

Gene Regulatory NetworksSoftwareTetrahymena thermophilaTranscriptomeComputational BiologyGene Expression Profiling

Identifiers

PMID40432793
PMCPMC12107436

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
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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.