Experiments
Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).
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Has reproduction · 80
Colorectal Cancer Prediction Based on Weighted Gene Co-Expression Network Analysis and Variational Auto-Encoder.
PMID 32825264 · PMC7563725 · Biomolecules · 2020 · 6 claims · 7 setups
Combining WGCNA hub genes and VAE 10-dimensional representation as features for an SVM classifier achieves high accuracy in predicting CRC
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Has reproduction · 55
Identification and verification of diagnostic biomarkers in recurrent pregnancy loss via machine learning algorithm and WGCNA.
PMID 37691920 · PMC10485775 · Frontiers in immunology · 2023 · 8 claims · 8 setups
352 DEGs (198 up-regulated, 154 down-regulated) were identified between RPL and control endometrial samples
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Has reproduction · 71
Interpretable artificial intelligence based on immunoregulation-related genes predicts prognosis and immunotherapy response in lung adenocarcinoma.
PMID 41048340 · PMC12491262 · Frontiers in bioinformatics · 2025 · 8 claims · 8 setups
IRG expression pattern clusters LUAD patients into groups with significantly different survival outcomes and immune cell infiltration
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Has reproduction · 49
LRP1 as a potential diagnostic and immunomodulatory target in endometriosis: evidence from multi-omics and single-cell analyses.
PMID 42064072 · PMC13124487 · Frontiers in immunology · 2026 · 8 claims · 8 setups
LRP1 is a hub gene with the highest diagnostic performance among 30 candidate hub genes identified by machine learning
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Has reproduction · 71
Comprehensive comparison of gene expression diversity among a variety of human stem cells.
PMID 36458020 · PMC9706419 · NAR genomics and bioinformatics · 2022 · 8 claims · 8 setups
Tissue origin has a stronger influence on gene expression in iPSCs than in other stem cell types
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Has reproduction · 55
Gene module regulation in dilated cardiomyopathy and the role of Na/K-ATPase.
PMID 35901050 · PMC9333241 · PloS one · 2022 · 7 claims · 7 setups
Several WGCNA gene co-expression modules are significantly associated with both LVEF and the DCM phenotype in heart failure patients.
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Has reproduction · 91
Exploring the key genetic association between chronic pancreatitis and pancreatic ductal adenocarcinoma through integrated bioinformatics.
PMID 37501719 · PMC10369079 · Frontiers in genetics · 2023 · 8 claims · 8 setups
CP and PDAC share a co-expression gene network identifiable via WGCNA on independent GEO datasets
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Has reproduction · 58
Identification of common genetic characteristics of rheumatoid arthritis and major depressive disorder by bioinformatics analysis and machine learning.
PMID 37415981 · PMC10320004 · Frontiers in immunology · 2023 · 7 claims · 8 setups
EAF1, SDCBP and RNF19B are common genetic characteristics (hub genes) shared by RA and MDD
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Has reproduction · 97
Identification of immune-related signatures and pathogenesis differences between thoracic aortic aneurysm patients with bicuspid versus tricuspid valves via weighted gene co-expression network analysis.
PMID 37883426 · PMC10602290 · PloS one · 2023 · 6 claims · 8 setups
TAA/TAV pathogenesis is more strongly associated with immune-related gene expression than TAA/BAV.
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Has reproduction · 80
Comprehensive analysis of transcriptomics and radiomics revealed the potential of TEDC2 as a diagnostic marker for lung adenocarcinoma.
PMID 39553728 · PMC11569783 · PeerJ · 2024 · 8 claims · 8 setups
WGCNA identified 214 key genes in the blue module most correlated with LUAD
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Has reproduction · 78
Machine learning and free energy clustering reveal PAH protein binding linked to AD risk.
PMID 41953002 · PMC13053772 · iScience · 2026 · 8 claims · 8 setups
PARP1, PTPN1, and ITGA4 are core PAH protein targets identified via PPI network analysis and XGBoost feature selection from AD-associated DEGs
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Has reproduction · 69
Machine learning-based identification of an immunotherapy-related signature to enhance outcomes and immunotherapy responses in melanoma.
PMID 39355255 · PMC11442245 · Frontiers in immunology · 2024 · 8 claims · 8 setups
66 consensus immunotherapy prognostic genes (CITPGs) were identified from the intersection of WGCNA modules, immunotherapy responder-vs-non-responder DEGs, and tumor-vs-normal DEGs
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Has reproduction · 100
Identification of a PRDM1-regulated T cell network to regulate atherosclerotic plaque inflammation.
PMID 41039608 · PMC12490039 · Genome medicine · 2025 · 7 claims · 7 setups
A distinct gene co-expression module with a prominent T cell signature is associated with unstable plaques.
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Identification of Four Potential Biomarkers Associated With Coronary Artery Disease in Non-diabetic Patients by Gene Co-expression Network Analysis.
PMID 32714363 · PMC7344232 · Frontiers in genetics · 2020 · 6 claims · 6 setups
The midnight blue module and the yellow module play vital roles in the pathogenesis of CAD in non-diabetic patients
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Has reproduction
A newly identified glycosyltransferase AsRCOM provides resistance to purple curl leaf disease in agave.
PMID 37936069 · PMC10629022 · BMC genomics · 2023 · 8 claims · 4 setups
Hypersensitive response (HR) accompanied by systemic acquired resistance is the primary contributor to resistance against purple curl leaf disease in agave
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Has reproduction · 76
Exploration of the shared diagnostic genes and molecular mechanism between obesity and atherosclerosis via bioinformatic analysis.
PMID 39825072 · PMC11742665 · Scientific reports · 2025 · 8 claims · 8 setups
56 shared genes with consistent expression trend were identified between OB and AS by intersecting WGCNA key module genes with DEGs
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Full-text index only
Revealing potential interfering genes between abdominal aortic aneurysm and periodontitis through machine learning and bioinformatics analysis.
PMID 40857330 · PMC12380325 · PloS one · 2025 · 6 claims · 8 setups
90 interacting genes were identified at the intersection of AAA DEGs and periodontitis WGCNA module genes
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Has reproduction · 86
Screening of core genes prognostic for sepsis and construction of a ceRNA regulatory network.
PMID 36855106 · PMC9976425 · BMC medical genomics · 2023 · 8 claims · 7 setups
RNA-seq of peripheral blood from 23 sepsis patients and 10 healthy controls identifies 1,044 DEmRNAs, 66 DEmiRNAs and 155 DElncRNAs.
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Has reproduction · 100
Gene co-expression network analysis in human spinal cord highlights mechanisms underlying amyotrophic lateral sclerosis susceptibility.
PMID 33707641 · PMC7970949 · Scientific reports · 2021 · 8 claims · 8 setups
WGCNA on control human cervical spinal cord RNA-seq identifies 13 co-expression modules (SC.M1-M13), each representing distinct biological processes or cell types.
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Has reproduction · 44
Weighted gene co-expression network analysis reveals that CXCL10, IRF7, MX1, RSAD2, and STAT1 are related to the chronic stage of spinal cord injury.
PMID 34532385 · PMC8421925 · Annals of translational medicine · 2021 · 8 claims · 7 setups
The brown co-expression module (775 genes) is the module most significantly associated with the chronic stage of SCI