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 · 58
Comprehensive analysis of peroxisome proliferator-activated receptors to predict the drug resistance, immune microenvironment, and prognosis in stomach adenocarcinomas.
PMID 38529307 · PMC10962337 · PeerJ · 2024 · 8 claims · 8 setups
PPARA, PPARD and PPARG are more abnormally expressed in STAD samples and cell lines compared to most of 32 cancer types in TCGA
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Has reproduction · 55
Identification of TYR, TYRP1, DCT and LARP7 as related biomarkers and immune infiltration characteristics of vitiligo via comprehensive strategies.
PMID 34107850 · PMC8806433 · Bioengineered · 2021 · 6 claims · 6 setups
TYR, TYRP1, DCT and LARP7 are biomarkers associated with vitiligo
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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 · 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 · 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 · 7 setups
TAA/TAV pathogenesis is more associated with immune-related gene expression than TAA/BAV, with two WGCNA gene modules (brown and blue) enriched for immune functions.
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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 · 67
Comprehensive Analysis of Cell Population Dynamics and Related Core Genes During Vitiligo Development.
PMID 33679890 · PMC7933673 · Frontiers in genetics · 2021 · 8 claims · 7 setups
Immune cell infiltration and abnormal gene expression are closely related to vitiligo pathogenesis
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Has reproduction · 40
PD-1 blockade potentiates neoadjuvant chemotherapy in NSCLC via increasing CD127(+) and KLRG1(+) CD8 T cells.
PMID 37231145 · PMC10213055 · NPJ precision oncology · 2023 · 8 claims · 4 setups
Adding PD-1 blockade to neoadjuvant chemotherapy (NAPC) increases tumor infiltration of CD20+ B cells, CD4+ T cells, CD4+CD127+ T cells, CD8+ T cells, CD8+CD127+ and CD8+KLRG1+ T cells, whereas NAC alone increases only CD20+ B cells.
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Has reproduction · 63
Creation of a Single Cell RNASeq Meta-Atlas to Define Human Liver Immune Homeostasis.
PMID 34335581 · PMC8322955 · Frontiers in immunology · 2021 · 7 claims · 7 setups
Independent human liver immune scRNA-seq datasets can be combined into an integrated meta-atlas in which all datasets co-cluster, despite differing cell-type proportions between studies.
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Has reproduction · 67
HArmonized single-cell RNA-seq Cell type Assisted Deconvolution (HASCAD).
PMID 37907883 · PMC10619225 · BMC medical genomics · 2023 · 6 claims · 5 setups
HASCAD, a DNN-based cell composition deconvolution model, predicts the fractions of up to 15 immune cell types from bulk RNA-seq.
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Has reproduction · 71
Parsimonious Gene Correlation Network Analysis (PGCNA): a tool to define modular gene co-expression for refined molecular stratification in cancer.
PMID 30993001 · PMC6459838 · NPJ systems biology and applications · 2019 · 8 claims · 7 setups
Retaining only the top ~3 most correlated edges per gene (EPG3) combined with FastUnfold clustering (termed PGCNA) produces gene co-expression modules with significantly better separation and enrichment of known biology than using all edges or other clustering methods.
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Has reproduction · 42
Machine learning-based identification of biomarkers and drugs in immunologically cold and hot pancreatic adenocarcinomas.
PMID 39152432 · PMC11328457 · Journal of translational medicine · 2024 · 7 claims · 8 setups
PAAD tumors can be consensus-clustered into immunologically hot and cold subtypes based on CIBERSORT-derived immune cell fractions, with significantly different survival outcomes.
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Has reproduction · 48
Bioinformatics Analysis of the Characteristics and Correlation of m6A Methylation in Breast Cancer Progression.
PMID 35655723 · PMC9148239 · Contrast media & molecular imaging · 2022 · 8 claims · 8 setups
Breast cancer samples can be divided into 4 m6A subtypes (quiescent, m6A methylation, protein-binding, mixed) based on expression of m6A-related genes, with consistent proportions across datasets
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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 · 63
Community assessment of methods to deconvolve cellular composition from bulk gene expression.
PMID 39191725 · PMC11350143 · Nature communications · 2024 · 8 claims · 4 setups
Most deconvolution methods accurately predict coarse-grained immune/stromal cell populations from bulk expression.
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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) were identified for HCM by intersecting DEGs with MR-derived HCM-associated eQTLs.
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Has reproduction · 48
Screening of Diagnostic Biomarkers and Immune Infiltration Characteristics Linking Rheumatoid Arthritis and Rosacea Based on Bioinformatics Analysis.
PMID 39104909 · PMC11299729 · Journal of inflammation research · 2024 · 8 claims · 8 setups
277 co-expressed DEGs shared between RA and rosacea are enriched in immune processes and chemokine-mediated signaling pathways
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Has reproduction · 93
5-methylcytosine RNA modification regulators-based patterns and features of immune microenvironment in acute myeloid leukemia.
PMID 38277218 · PMC10911375 · Aging · 2024 · 8 claims · 8 setups
Most of the 17 m5C regulators are differentially expressed between AML and normal samples and correlate with AML prognosis.
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Has reproduction · 50
STAT1 and IL-7 as potential diagnostic biomarkers for distinguishing high-grade from low-grade serous ovarian cancer: a multi-cohort analysis.
PMID 42058211 · PMC13120972 · Frontiers in immunology · 2026 · 7 claims · 6 setups
STAT1 and IL-7 are differentially expressed immune-related genes that can distinguish HGSOC from LGSOC and may serve as ancillary diagnostic biomarkers.
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Has reproduction · 71
Machine Learning-Based Integrated Analysis of PANoptosis Patterns in Acute Myeloid Leukemia Reveals a Signature Predicting Survival and Immunotherapy.
PMID 38322112 · PMC10846924 · International journal of clinical practice · 2024 · 7 claims · 7 setups
AML patients can be categorized into two distinct PANRG-based clusters with differing prognosis and immune characteristics