Evidence map›Paper›PMID 38370125›Full record

ArticlePatterns (New York, N.Y.)2024

GAiN: An integrative tool utilizing generative adversarial neural networks for augmented gene expression analysis.

Michael R Waters, Matthew Inkman, Kay Jayachandran, Roman M Kowalchuk, Clifford Robinson, Julie K Schwarz, S Joshua Swamidass, Obi L Griffith, Jeffrey J Szymanski, Jin Zhang

Open access · goldAbstract read
In one paragraph

Article in Patterns (New York, N.Y.), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing papers in PubMed
4.0field-weighted citation impact, top 8% of its field
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

7 citing papers in PubMed, 6 citations in OpenAlex.

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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

10 authors at 3 institutions in 1 country.

Michael R WatersDepartment of Radiation Oncology, Washington University School of Medicine, St. Louis, MO 63108, USA.
Matthew InkmanDepartment of Radiation Oncology, Washington University School of Medicine, St. Louis, MO 63108, USA.
Kay JayachandranDepartment of Radiation Oncology, Washington University School of Medicine, St. Louis, MO 63108, USA.
Roman M KowalchukDepartment of Radiation Oncology, Mayo Clinic, Rochester, MN 55905, USA.
Clifford RobinsonDepartment of Radiation Oncology, Washington University School of Medicine, St. Louis, MO 63108, USA.
Julie K SchwarzDepartment of Radiation Oncology, Washington University School of Medicine, St. Louis, MO 63108, USA.
S Joshua SwamidassDepartment of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
Obi L GriffithDepartment of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
Jeffrey J SzymanskiDepartment of Radiation Oncology, Washington University School of Medicine, St. Louis, MO 63108, USA.
Jin ZhangDepartment of Radiation Oncology, Washington University School of Medicine, St. Louis, MO 63108, USA.
Washington University in St. Louis · USJames S. McDonnell Foundation · USMayo Clinic · US

Funding

Washington University (WU) ROBIN Center: MicroEnvironment and Tumor Effects Of Radiotherapy (METEOR)U54CA274318 · NCI · WASHINGTON UNIVERSITY · PI Clifford Grant Robinson · 2023 to 2026
$7.7M
Integrating multi-omics, imaging, and longitudinal data to predict radiation response in cervical cancerR01CA276955 · NCI · WASHINGTON UNIVERSITY · PI Jin Zhang · 2023 to 2026
$2.1M
HPV genomic structure in cervical cancer radiation response and recurrence detectionR37CA279596 · NCI · WASHINGTON UNIVERSITY · PI Jin Zhang · 2023 to 2026
$2.0M
HPV alternative splicing in cervical cancer radiation responseK22CA237839 · NCI · WASHINGTON UNIVERSITY · PI ZHANG, JIN · 2021 to 2023
$460k
Deep learning in cervical cancer radiogenomicsR21CA264343 · NCI · WASHINGTON UNIVERSITY · PI ZHANG, JIN · 2022 to 2023
$401k
NCI NIH HHS K22 CA237839NCI NIH HHS R01 CA276955NCI NIH HHS R21 CA264343NCI NIH HHS R37 CA279596NCI NIH HHS U54 CA274318
6 · The paper itself

Abstract

Big genomic data and artificial intelligence (AI) are ushering in an era of precision medicine, providing opportunities to study previously under-represented subtypes and rare diseases rather than categorize them as variances. However, clinical researchers face challenges in accessing such novel technologies as well as reliable methods to study small datasets or subcohorts with unique phenotypes. To address this need, we developed an integrative approach, GAiN, to capture patterns of gene expression from small datasets on the basis of an ensemble of generative adversarial networks (GANs) while leveraging big population data. Where conventional biostatistical methods fail, GAiN reliably discovers differentially expressed genes (DEGs) and enriched pathways between two cohorts with limited numbers of samples (n = 10) when benchmarked against a gold standard. GAiN is freely available at GitHub. Thus, GAiN may serve as a crucial tool for gene expression analysis in scenarios with limited samples, as in the context of rare diseases, under-represented populations, or limited investigator resources.

Indexed as

deep learning GANsdifferential gene expressiongene expression analysisgenerative modelinghigh-throughput sequencing datapathway enrichmentsmall sample sizesstructural gene expression patternssynthetic RNA expression datasets

Identifiers

PMID38370125
PMCPMC10873154
OpenAlexW4390674048

What Socratic holds

Textmetadata
LicenceCC BY-NC-ND
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 Socratic graph.