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 · 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 · 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 · 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 · 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
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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 · 75
Integrative analysis reveals chemokines CCL2 and CXCL5 mediated shear stress-induced aortic dissection formation.
PMID 38163105 · PMC10757018 · Heliyon · 2024 · 8 claims · 8 setups
Integration of three AD RNA-seq datasets identifies 150 common DEGs (100 down-regulated, 50 up-regulated) enriched for blood vessel morphogenesis, muscle structure/tissue development, and chemotaxis.
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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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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 · 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
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Human disease classification in the postgenomic era: a complex systems approach to human pathobiology.
PMID 17625512 · PMC1948102 · Molecular systems biology · 2007 · 8 claims · 5 setups
Current syndromic disease classification lacks specificity despite historically serving clinicians well
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Has reproduction · 62
A comparative gene co-expression analysis using self-organizing maps on two congener filmy ferns identifies specific desiccation tolerance mechanisms associated to their microhabitat preference.
PMID 32019526 · PMC7001327 · BMC plant biology · 2020 · 8 claims · 6 setups
H. caudiculatum (lower canopy) exhibits about twice as many differentially expressed genes as H. dentatum (upper canopy), with a higher proportion of both increased and decreased gene abundance during dehydration.
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Has reproduction · 67
Heterogeneity and Differentiation Trajectories of Infiltrating CD8+ T Cells in Lung Adenocarcinoma.
PMID 36358600 · PMC9658355 · Cancers · 2022 · 7 claims · 8 setups
Infiltrating CD8+ T cells in LUAD can be divided into ten transcriptionally distinct subsets: eight cytotoxic (CTL) subsets, one naive-like (NTL) subset, and one exhausted (ETL) subset.
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Has reproduction · 56
Modulation of HERV Expression by Four Different Encephalitic Arboviruses during Infection of Human Primary Astrocytes.
PMID 36423114 · PMC9694637 · Viruses · 2022 · 6 claims · 7 setups
The four arboviruses commonly induce upregulation of HERVs in human primary astrocytes, with 15 HERVs co-modulated by all four viruses, including highly upregulated HERV4_4q22.1