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).

Publications 1.3k Datasets 392.5k Experiments 15

System / cell line: interaction ✕ Assay: ssgsea ✕ Clear

Spatial transcriptome and single-cell sequencing reveal the role of nucleotide metabolism in breast cancer progression and tumor microenvironment.

PMID 41613532 · PMC12847018 · Frontiers in oncology · 2025 · 7 claims · 8 setups

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Tumor cells show significantly upregulated nucleotide metabolic activity, allowing stratification into NUhighepi and NUlowepi subgroups

tcga-brca breast scrna-seq epithelial ssgsea single-cell cell-cell
Integrative bulk and single-cell transcriptomics link EZH2 to immunosuppressive programs and tumor-Treg crosstalk in castration-resistant prostate cancer.

PMID 41710887 · PMC12909565 · Frontiers in immunology · 2026 · 8 claims · 8 setups

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Higher EZH2 expression is associated with adverse clinical outcomes in bulk PCa/CRPC cohorts

tcga-prad su2c gse264573 gse137829 bulk scrna-seq ligand-receptor
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

Has reproduction · 80

A neutrophil-related co-expression gene module (blue module) is significantly associated with aSAH occurrence

peripheral genes overlapping neutrophil-related microarray weighted kegg
Emergent dynamics of underlying regulatory network links EMT and androgen receptor-dependent resistance in prostate cancer.

PMID 36851919 · PMC9957767 · Computational and structural biotechnology journal · 2023 · 8 claims · 7 setups

Has reproduction · 78

Simulations of the EMT-AR crosstalk network reveal four possible phenotypes: epithelial-sensitive (ES), epithelial-resistant (ER), mesenchymal-resistant (MR), and mesenchymal-sensitive (MS), with MS occurring rarely

gene racipe clinical tcga racipe influence principal
Differential bone morphology and hypoxia activity in skeletal metastases of ER(+) and ER(-) breast cancer.

PMID 39572705 · PMC11582807 · Communications biology · 2024 · 8 claims · 8 setups

Has reproduction · 68

ER− MDA-MB-231 breast cancer forms more osteolytic bone metastases than ER+ MCF-7 breast cancer

mcf-7 breast bone tumor-free immunofluorescence co-culture rna-seq
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

Has reproduction · 97

TAA/TAV pathogenesis is more strongly associated with immune-related gene expression than TAA/BAV.

aortic genes wgcna gene cibersort
Exploration of effective biomarkers for venous thrombosis embolism in Behçet's disease based on comprehensive bioinformatics analysis.

PMID 38987624 · PMC11236978 · Scientific reports · 2024 · 6 claims · 8 setups

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Four hub genes (E2F1, GATA3, HDAC5, MSH2) serve as diagnostic biomarkers for VTE in BD with high accuracy (AUC 0.816)

peripheral degs candidate microarray weighted protein–protein
Single-cell transcriptomic analysis reveals intra-tumoral heterogeneity and immunotherapy strategies in high-grade serous ovarian cancer.

PMID 41907410 · PMC13018870 · iScience · 2026 · 8 claims · 8 setups

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scRNA-seq of 17 HGSOC tissue samples reveals seven major cell types and extensive intra-tumoral heterogeneity

hgsoc epithelial tcga gse165897 single-cell copy kegg
Single-cell analysis highlights the role of CD4(+) IFN-I-related T cells in Behcet's uveitis during Interferonα-2a therapy.

PMID 42021381 · PMC13238117 · Biology direct · 2026 · 6 claims · 8 setups

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CD4+ IFN-I-related T cells are significantly decreased in active BD patients and restored after IFNα-2a therapy

pbmcs sorted skin scrna-seq scrna-seq bulk cell-cell
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

Has reproduction · 71

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

tcga-blca famc1-3 differentially gse32894 bulk consensus gene
Cancer-wide in silico analyses using differentially expressed genes demonstrate the functions and clinical relevance of JAG, DLL, and NOTCH.

PMID 39074091 · PMC11285958 · PloS one · 2024 · 7 claims · 8 setups

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JAG, DLL, and NOTCH family gene/protein expression varies diversely across 15 cancer types relative to normal tissue, sometimes discordant between mRNA and protein levels.

tumor degs cancer jag bulk proteomics gene
Development and validation of an oxidative phosphorylation based prognostic model revealing tumor progression and immune microenvironment in lung adenocarcinoma.

PMID 41670771 · PMC12996521 · Discover oncology · 2026 · 8 claims · 8 setups

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OXPHOS activity is significantly elevated in LUAD tumor tissue compared to adjacent normal tissue

tcga-luad geo lung single-cell bulk ssgsea cibersort
Multimodal learning reveals plants' hidden sensory integration logic.

PMID 41714925 · PMC13032346 · BMC genomics · 2026 · 8 claims · 8 setups

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CoMM-BIP (Contrastive Multi-Modal learning with Biologically Informed Priors) integrates transcriptomic, metabolomic, and phenomic data using pathway-guided attention, information-theoretic disentanglement, and domain-aware augmentations

tomato multimodal transcriptomics metabolomics
Heterogeneity of cancer-associated fibroblasts in head and neck squamous cell carcinoma.

PMID 37320872 · PMC10277597 · Translational oncology · 2023 · 8 claims · 9 setups

Has reproduction · 50

Seven distinct CAF subsets exist in HNSCC, identified via integration of scRNA-seq, bulk transcriptomic, and spatial transcriptomic data.

hnscc tcga-hnscc caf fibroblast single-cell bulk spatial
Single-Cell Sequencing Reveals γδT Cell Heterogeneity Under Distinct Microsatellite Statuses as a Potential Biomarker for Immunotherapy and Prognosis in Colorectal Cancer.

PMID 42074506 · PMC13116210 · Genes · 2026 · 7 claims · 8 setups

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γδT cells in colorectal cancer form five distinct subsets (C0_FCER1G, C1_IL7R, C2_CD81, C3_TOP2A, C4_CXCL13) with distinct marker genes and functional states

crc γδt epithelial c4_cxcl13 single-cell differential pseudotime

Experiments

Spatial transcriptome and single-cell sequencing reveal the role of nucleotide metabolism in breast cancer progression and tumor microenvironment.

Integrative bulk and single-cell transcriptomics link EZH2 to immunosuppressive programs and tumor-Treg crosstalk in castration-resistant prostate cancer.

Specific signature biomarkers highlight the potential mechanisms of circulating neutrophils in aneurysmal subarachnoid hemorrhage.

Emergent dynamics of underlying regulatory network links EMT and androgen receptor-dependent resistance in prostate cancer.

Differential bone morphology and hypoxia activity in skeletal metastases of ER(+) and ER(-) breast cancer.

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.

Exploration of effective biomarkers for venous thrombosis embolism in Behçet's disease based on comprehensive bioinformatics analysis.

Single-cell transcriptomic analysis reveals intra-tumoral heterogeneity and immunotherapy strategies in high-grade serous ovarian cancer.

Single-cell analysis highlights the role of CD4(+) IFN-I-related T cells in Behcet's uveitis during Interferonα-2a therapy.

Assessment tool based on fatty acid metabolic signatures for predicting the prognosis and treatment response in bladder cancer.

Cancer-wide in silico analyses using differentially expressed genes demonstrate the functions and clinical relevance of JAG, DLL, and NOTCH.

Development and validation of an oxidative phosphorylation based prognostic model revealing tumor progression and immune microenvironment in lung adenocarcinoma.

Multimodal learning reveals plants' hidden sensory integration logic.

Heterogeneity of cancer-associated fibroblasts in head and neck squamous cell carcinoma.

Single-Cell Sequencing Reveals γδT Cell Heterogeneity Under Distinct Microsatellite Statuses as a Potential Biomarker for Immunotherapy and Prognosis in Colorectal Cancer.