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 · 95
Pathway-targeting gene matrix for Drosophila gene set enrichment analysis.
PMID 34710184 · PMC8553153 · PloS one · 2021 · 8 claims · 4 setups
Gene matrix files for GSEA are largely unavailable for Drosophila, limiting pathway-level enrichment analysis in this model organism
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Has reproduction · 78
Meta-analysis of gene expression profiles of lean and obese PCOS to identify differentially regulated pathways and risk of comorbidities.
PMID 32695266 · PMC7352056 · Computational and structural biotechnology journal · 2020 · 8 claims · 8 setups
The majority of differentially expressed genes in PCOS are downregulated regardless of tissue type and phenotype
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Cross species genomic analysis identifies a mouse model as undifferentiated pleomorphic sarcoma/malignant fibrous histiocytoma.
PMID 19956606 · PMC2779485 · PloS one · 2009 · 8 claims · 7 setups
A 100-gene signature from LSL-KrasG12D;Trp53Flox/Flox mouse sarcomas (vs normal muscle) is specifically and significantly enriched in human MFH but not other soft tissue sarcoma subtypes across three independent human datasets.
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Has reproduction · 50
Integrative analysis of transcriptomic data reveals a predictive gene signature for chemoradiotherapy response in rectal cancer.
PMID 41550766 · PMC12803930 · iScience · 2026 · 8 claims · 5 setups
A 186-gene signature derived from six GEO transcriptomic datasets predicts nCRT response in LARC with AUC 0.80 in cross-validation
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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 · 69
COVID-19 vaccination atlas using an integrative systems vaccinology approach.
PMID 40456760 · PMC12130191 · NPJ vaccines · 2025 · 8 claims · 6 setups
mRNA vaccines induce transient but strong immune responses after booster doses
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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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GeneTrail--advanced gene set enrichment analysis.
PMID 17526521 · PMC1933132 · Nucleic acids research · 2007 · 8 claims · 2 setups
GeneTrail is a comprehensive, easy-to-use web-based tool for gene set enrichment analysis supporting both Over-Representation Analysis (ORA) and Gene Set Enrichment Analysis (GSEA)
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Has reproduction · 48
Indoleamine 2, 3-Dioxygenase 1 and CD8 Expression Profiling Revealed an Immunological Subtype of Colon Cancer With a Poor Prognosis.
PMID 33425745 · PMC7793995 · Frontiers in oncology · 2020 · 7 claims · 6 setups
The CD8A-high/IDO1-high colon cancer subtype (group IV*) has the worst survival despite high CD8 infiltrates.
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Has reproduction · 100
A comprehensive framework for analysis of microRNA sequencing data in metastatic colorectal cancer.
PMID 35047825 · PMC8759566 · NAR cancer · 2022 · 7 claims · 7 setups
Five miRNAs (Mir-210_3p, Mir-191_5p, Mir-8-P1b_3p [miR-141-3p], Mir-1307_5p, Mir-155_5p) are up-regulated at multiple metastatic sites in colorectal cancer.
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Has reproduction · 19
Bioinformatics Strategies to Identify Shared Molecular Biomarkers That Link Ischemic Stroke and Moyamoya Disease with Glioblastoma.
PMID 36015199 · PMC9413912 · Pharmaceutics · 2022 · 8 claims · 8 setups
Shared differentially expressed genes link glioblastoma with ischemic stroke and with moyamoya disease, revealing molecular associations among the diseases.
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Has reproduction · 71
Identification of the shared hub gene signatures and molecular mechanisms between HIV-1 and pulmonary arterial hypertension.
PMID 38528047 · PMC10963360 · Scientific reports · 2024 · 7 claims · 7 setups
HIV-1 and PAH share 109 co-expressed genes primarily enriched in type I interferon (IFN) pathways.
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Has reproduction · 84
Network Controllability Reveals Key Mitigation Points for Tumor-Promoting Signaling in Tumor-Educated Platelets.
PMID 41226816 · PMC12609506 · International journal of molecular sciences · 2025 · 8 claims · 6 setups
TEPs in NSCLC show 111 upregulated and 108 downregulated genes versus non-cancer control platelets, enriched in ECM interaction, cytoskeleton, immune signaling, and platelet activation pathways.
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Has reproduction · 62
CASK loss of function differentially regulates neuronal maturation and synaptic function in human induced cortical excitatory neurons.
PMID 36262316 · PMC9574418 · iScience · 2022 · 7 claims · 8 setups
CASK LOF increases neuronal complexity (neurite overgrowth) in developing/immature human excitatory neurons
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Has reproduction · 71
Assessment tool based on fatty acid metabolic signatures for predicting the prognosis and treatment response in bladder cancer.
PMID 38076064 · PMC10703629 · Heliyon · 2023 · 8 claims · 8 setups
Consensus clustering of prognosis-related fatty acid metabolism genes (FAMGs) identifies three molecular subtypes of BLCA (FAMC1, FAMC2, FAMC3) with distinct prognoses and tumor microenvironments
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Has reproduction · 50
Transcriptome profiling of osteoclast subsets associated with arthritis: A pathogenic role of CCR2(hi) osteoclast progenitors.
PMID 36591261 · PMC9797520 · Frontiers in immunology · 2022 · 8 claims · 6 setups
CCR2hi and CCR2lo periarticular bone marrow OCP subsets show a disparate transcriptome (863 differentially expressed genes)
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Has reproduction · 66
A global database for modeling tumor-immune cell communication.
PMID 37438390 · PMC10338499 · Scientific data · 2023 · 7 claims · 6 setups
TICCom integrates 739 experimentally-validated or manually-curated TIC interactions collected from more than 3,000 literatures
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A taxonomy of epithelial human cancer and their metastases.
PMID 20017941 · PMC2806369 · BMC medical genomics · 2009 · 8 claims · 6 setups
Unsupervised hierarchical clustering of 1566 primary epithelial tumors yields large tissue-enriched clusters (breast, colon/GI, lung, ovary, kidney) plus smaller prostate, thyroid-kidney, and mixed clusters
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Has reproduction
Differential Infiltration of Key Immune T-Cell Populations Across Malignancies Varying by Immunogenic Potential and the Likelihood of Response to Immunotherapy.
PMID 39682743 · PMC11640164 · Cells · 2024 · 7 claims · 4 setups
Immune-activation-related T-cell populations (APA, TRM, stem-like, early/late dysfunctional T-cells) are more heavily infiltrated in ICI-responsive malignancies (melanoma, bladder) than in poorly responsive ones (ovarian, pancreatic).
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Has reproduction · 70
Spatial transcriptomics reveals the molecular signatures of prodromal and advanced α-synucleinopathy.
PMID 41736854 · PMC12927100 · iScience · 2026 · 8 claims · 6 setups
Induction of aSyn pathology in rodent brainstem at the early/prodromal stage triggers upregulation of energy metabolism pathways (glycolysis, oxidative phosphorylation, fatty acid metabolism)