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 · 73
Identification of intrinsic genes across general hypertension, hypertension with left ventricular remodeling, and uncontrolled hypertension.
PMID 36277786 · PMC9582241 · Frontiers in cardiovascular medicine · 2022 · 7 claims · 8 setups
FBXW4 and 13 other genes are uniquely enriched in the general hypertension group
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Has reproduction · 83
Discovery and validation of molecular patterns and immune characteristics in the peripheral blood of ischemic stroke patients.
PMID 38650649 · PMC11034498 · PeerJ · 2024 · 8 claims · 8 setups
188 differentially expressed genes (DEGs) between IS and control blood samples were identified and enriched in immune-related biological pathways
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Has reproduction · 45
NUSAP1 Could be a Potential Target for Preventing NAFLD Progression to Liver Cancer.
PMID 35431924 · PMC9010788 · Frontiers in pharmacology · 2022 · 7 claims · 8 setups
NUSAP1 is a hub gene linking NAFLD fibrosis progression and NAFLD-associated HCC
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Has reproduction · 85
Integrated Analysis of Multiple Microarrays Based on Raw Data Identified Novel Gene Signatures in Recurrent Implantation Failure.
PMID 35197930 · PMC8859149 · Frontiers in endocrinology · 2022 · 6 claims · 7 setups
Robust Rank Aggregation (RRA) can integrate DEG lists from multiple independent RIF microarray datasets to identify robust DEGs.
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Has reproduction · 20
Exploring the role and mechanism of Astragalus membranaceus and radix paeoniae rubra in idiopathic pulmonary fibrosis through network pharmacology and experimental validation.
PMID 37666859 · PMC10477296 · Scientific reports · 2023 · 8 claims · 8 setups
AM and RPR (Huangqi-Chishao decoction) alleviate bleomycin-induced pathological lung fibrotic damage in rats
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Has reproduction · 86
Molecular Classification Models for Triple Negative Breast Cancer Subtype Using Machine Learning.
PMID 34575658 · PMC8472680 · Journal of personalized medicine · 2021 · 7 claims · 4 setups
TNBC can be divided into four gene-expression-defined subtypes: BLIA, BLIS, MES, and LAR
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Has reproduction · 75
Identification and analysis of genes associated with epithelial ovarian cancer by integrated bioinformatics methods.
PMID 34143800 · PMC8213194 · PloS one · 2021 · 8 claims · 7 setups
306 overlapping DEGs (265 up-regulated, 41 down-regulated) were identified from three independent GEO microarray datasets comparing EOC and adjacent normal ovarian tissue
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Has reproduction · 80
Specific signature biomarkers highlight the potential mechanisms of circulating neutrophils in aneurysmal subarachnoid hemorrhage.
PMID 36438795 · PMC9685413 · Frontiers in pharmacology · 2022 · 8 claims · 8 setups
A neutrophil-related co-expression gene module (blue module) is significantly associated with aSAH occurrence
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Has reproduction · 78
SPRR1B+ keratinocytes prime oral mucosa for rapid wound healing via STAT3 activation.
PMID 39300285 · PMC11413210 · Communications biology · 2024 · 8 claims · 8 setups
A shared wound healing gene set (P2-WHGs, 146 genes) is constitutively expressed in uninjured oral mucosa but not in uninjured skin
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Has reproduction · 74
Identification and validation of a metabolic-related gene risk model predicting the prognosis of lung, colon, and breast cancers.
PMID 39779736 · PMC11711664 · Scientific reports · 2025 · 8 claims · 8 setups
540 DEGs overlap across breast, colorectal, and lung cancers out of 11,384 DEGs analyzed
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Has reproduction · 64
Comprehensive bioinformatics analysis and experimental verification identify mitochondrial gene Dgat2 as a novel therapeutic biomarker for myocardial ischemia-reperfusion.
PMID 40510478 · PMC12159077 · Frontiers in endocrinology · 2025 · 8 claims · 8 setups
Dgat2 is a hub mitochondria-related differentially expressed gene (MitoDEG) that can serve as a novel biomarker and therapeutic target in MI/RI
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Has reproduction · 88
Transcriptomic Data Meta-Analysis Sheds Light on High Light Response in Arabidopsis thaliana L.
PMID 35457273 · PMC9026532 · International journal of molecular sciences · 2022 · 7 claims · 6 setups
Meta-analysis of five transcriptomic experiments identified 1151 differentially expressed genes that compose a coordinated gene network responding to high light stress
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Has reproduction · 75
Identification of Key Differentially Expressed Genes in Arabidopsis thaliana Under Short- and Long-Term High Light Stress.
PMID 40869111 · PMC12386182 · International journal of molecular sciences · 2025 · 8 claims · 6 setups
Meta-analysis of 21 experiments covering 58 HL conditions yielded ~218,000 DEG instances corresponding to ~19,000 unique A. thaliana genes
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Has reproduction · 85
Integration of multi-omics and machine learning strategies identifies immune related candidate biomarkers in inflammation-associated hypertrophic cardiomyopathy.
PMID 41080564 · PMC12510942 · Frontiers in immunology · 2025 · 8 claims · 8 setups
Seven key immune-related genes (RNF165, SNCA, SRGN, MARCO, STEAP4, SIGLEC9, TKT) are associated with HCM by intersecting DEGs with MR-identified eQTLs
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Has reproduction · 59
Comparison between short-term stress and long-term adaptive responses reveal common paths to molecular adaptation.
PMID 35243257 · PMC8873613 · iScience · 2022 · 8 claims · 7 setups
Short-term stress and long-term adaptations share common metabolic pathways
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Has reproduction · 74
Autoencoder Networks Decipher the Association between Lung Cancer and Alzheimer's Disease.
PMID 36518809 · PMC9744611 · Computational intelligence and neuroscience · 2022 · 7 claims · 6 setups
AE networks trained on the 266 shared DEGs reveal a comorbidity (positive correlation) relationship between Alzheimer's disease and lung cancer, rather than the inverse relationship suggested by prior epidemiological studies.
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Has reproduction · 50
Wx: a neural network-based feature selection algorithm for transcriptomic data.
PMID 31324856 · PMC6642261 · Scientific reports · 2019 · 8 claims · 8 setups
The Wx algorithm ranks genes using a DI score reflecting each gene's classification power for distinguishing two groups.
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Has reproduction · 100
Exploring Gene Expression Patterns in Alzheimer's Disease Using a Human Microarray Data Meta-Analysis.
PMID 41744654 · PMC12938635 · Biology · 2026 · 7 claims · 7 setups
A meta-analysis of eight microarray studies (10 sub-studies) produced a combined list of 4218 statistically significant DEGs between AD and healthy brain at an adjP cut-off of 0.001
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Has reproduction · 88
From bud formation to flowering: transcriptomic state defines the cherry developmental phases of sweet cherry bud dormancy.
PMID 31830909 · PMC6909552 · BMC genomics · 2019 · 7 claims · 7 setups
Flower bud developmental stages (organogenesis, paradormancy, endodormancy, dormancy release, ecodormancy) are defined by distinct, stage-specific gene expression programs
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Has reproduction · 81
CCL8 as a promising prognostic factor in diffuse large B-cell lymphoma via M2 macrophage interactions: A bioinformatic analysis of the tumor microenvironment.
PMID 36072582 · PMC9441746 · Frontiers in immunology · 2022 · 8 claims · 8 setups
Higher stromal and ESTIMATE scores are associated with favorable prognosis in DLBCL