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 17

System / cell line: cohort ✕ Assay: ligand-receptor ✕ Clear

DLX2 marks an immunosuppressive dendritic-cell program that reshapes cytotoxic immunity and marks a tolerogenic microenvironment in lung adenocarcinoma.

PMID 41761000 · PMC13043845 · Discover oncology · 2026 · 8 claims · 8 setups

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Neuroactive ligand–receptor signaling is among the most significantly upregulated pathways in LUAD relative to normal lung tissue.

tcga-luad tcga luad dendritic-cell bulk survival pan-cancer
Multi-cohort and single-cell profiling of aging genes reveals prognostic and therapeutic targets in breast cancer.

PMID 41732271 · PMC12924738 · iScience · 2026 · 8 claims · 7 setups

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The eight-gene MLAG signature outperforms 100 previously published prognostic models across 12 independent breast cancer cohorts

tcga-brca senescent normal single-cell machine univariate 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
Identifying clinically relevant cell state interactions in the tumor microenvironment of IDH-mutant gliomas using CSI-TME.

PMID 41807578 · PMC13230996 · Molecular systems biology · 2026 · 7 claims · 8 setups

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CSI-TME is a computational pipeline that deconvolves bulk tumor RNA-seq into cell-type-specific expression (via CODEFACS), infers transcriptional states per cell type via ICA, and identifies IC pairs from two cell types whose joint activity is associated with survival via Cox regression

idh-mutant tcga cgga deconvolved scrna-seq bulk independent
Clustering and machine learning-based integration identify cancer associated fibroblasts genes' signature in head and neck squamous cell carcinoma.

PMID 37065499 · PMC10098459 · Frontiers in genetics · 2023 · 8 claims · 8 setups

Has reproduction · 63

Clustering of 31 CAFs genes across 868 HNSCC samples identifies two distinct molecular patterns (C1, C2) with different survival outcomes

hnscc combined gse164690 tcga-hnsc ssgsea unsupervised immune
A single-cell atlas characterizes dysregulation of the bone marrow immune microenvironment associated with outcomes in multiple myeloma.

PMID 41514053 · PMC12858409 · Nature cancer · 2026 · 8 claims · 6 setups

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Generated a single-cell Immune Atlas of 1,397,272 BM cells from 337 NDMM participants (263 discovery, 74 validation) using scRNA-seq

cd138 bone ndmm single-cell cytogenetic disease
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
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
Mitochondrial DNA methylation predicts immunotherapy response and prognosis in lung adenocarcinoma: evidence from scRNA-Seq and machine learning.

PMID 41663976 · PMC12997902 · BMC cancer · 2026 · 8 claims · 8 setups

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Differentially expressed MTDM-related genes (DEMTDMRGs) are significantly enriched in cell cycle regulation, ferroptosis, and ABC transporter pathways

luad demtdmrgs gse131907 wgcna kegg univariate
DeCAF defines clinical fibroblast subtypes and multidimensional tumor-stroma crosstalk shaping prognosis and immunotherapy response.

PMID 41707654 · PMC12923980 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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DeCAF is a single-sample kTSP classifier using 9 TSP gene pairs that predicts proCAF vs restCAF subtypes from bulk expression data

pdac cptac external elyada-sc bulk single-sample classifier
Assessing personalized molecular portraits underlying endothelial-to-mesenchymal transition within pulmonary arterial hypertension.

PMID 39462326 · PMC11513636 · Molecular medicine (Cambridge, Mass.) · 2024 · 8 claims · 8 setups

Has reproduction · 81

scRNA-seq of PAH and control lung tissue identifies nine distinct cell populations with high heterogeneity in composition, function, distribution, and communication

lung pah scrna-seq-derived endothelial scrna-seq bulk cell-cell
Unveiling the NEFH+ malignant cell subtype: Insights from single-cell RNA sequencing in prostate cancer progression and tumor microenvironment interactions.

PMID 39759507 · PMC11695424 · Frontiers in immunology · 2024 · 8 claims · 8 setups

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A malignant cell subtype in PCa with high expression of NEFH was identified, located at the differentiation terminal, showing higher malignancy and association with advanced tumor lesions.

pca malignant tcga mda single-cell infercnv pseudotime
MAZ-mediated tumor progression and immune evasion in hormone receptor-positive breast cancer: Targeting tumor microenvironment and PCLAF+ subtype-specific therapy.

PMID 39805182 · PMC11780959 · Translational oncology · 2025 · 6 claims · 8 setups

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A C3 PCLAF+ tumor cell subtype identified by scRNA-seq shows high proliferation/differentiation potential and is linked to aggressive tumor behavior and poor prognosis in HR+BC

hr+bc mda-mb-361 tcga scrna-seq cellchat pyscenic
SLC25A37 as a novel therapeutic target for benign prostatic hyperplasia: integrative analyses of single-cell RNA sequencing and genome-wide association studies.

PMID 41726128 · PMC12917586 · Open medicine (Warsaw, Poland) · 2026 · 8 claims · 8 setups

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SLC25A37 is causally associated with increased BPH risk, supported by MR, Bayesian colocalization, and reverse MR analyses

prostate gwas eqtl bph single-cell mendelian bayesian
Hypoxia-associated genes as predictors of outcomes in gastric cancer: a genomic approach.

PMID 40129974 · PMC11931070 · Frontiers in immunology · 2025 · 8 claims · 8 setups

Has reproduction · 96

A prognostic model built from five H1-specific hypoxia-associated transcription factors (EHF, EIF1AD, GLA, KEAP1, MAGED2) predicts overall survival in STAD, with high-risk patients showing significantly worse OS.

gastric gene scrna-seq tcga single-cell wgcna cell-cell
Integrating single-cell and bulk transcriptomes identifies B cell features associated with neoadjuvant chemoradiotherapy sensitivity in rectal cancer.

PMID 41484196 · PMC12800305 · Scientific reports · 2026 · 8 claims · 8 setups

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A B cell subpopulation co-expressing HLA-DRB5, HLA-DQA2, HLA-DQB1, CD74, and ACTG1 is significantly associated with favorable nCRT response in rectal cancer

larc scrna-seq scissor+ single-cell bulk pseudotime
Deciphering the Immune Microenvironment at the Forefront of Tumor Aggressiveness by Constructing a Regulatory Network with Single-Cell and Spatial Transcriptomic Data.

PMID 38254989 · PMC10815467 · Genes · 2024 · 7 claims · 8 setups

Has reproduction · 85

High expression of transcription factors FOXA1 and EZH2 in malignant cells at the invasive front plays a key role in driving tumor progression

breast er+ epithelial malignant scrna-seq spatial copy

Experiments

DLX2 marks an immunosuppressive dendritic-cell program that reshapes cytotoxic immunity and marks a tolerogenic microenvironment in lung adenocarcinoma.

Multi-cohort and single-cell profiling of aging genes reveals prognostic and therapeutic targets in breast cancer.

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

Identifying clinically relevant cell state interactions in the tumor microenvironment of IDH-mutant gliomas using CSI-TME.

Clustering and machine learning-based integration identify cancer associated fibroblasts genes' signature in head and neck squamous cell carcinoma.

A single-cell atlas characterizes dysregulation of the bone marrow immune microenvironment associated with outcomes in multiple myeloma.

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

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

Mitochondrial DNA methylation predicts immunotherapy response and prognosis in lung adenocarcinoma: evidence from scRNA-Seq and machine learning.

DeCAF defines clinical fibroblast subtypes and multidimensional tumor-stroma crosstalk shaping prognosis and immunotherapy response.

Assessing personalized molecular portraits underlying endothelial-to-mesenchymal transition within pulmonary arterial hypertension.

Unveiling the NEFH+ malignant cell subtype: Insights from single-cell RNA sequencing in prostate cancer progression and tumor microenvironment interactions.

MAZ-mediated tumor progression and immune evasion in hormone receptor-positive breast cancer: Targeting tumor microenvironment and PCLAF+ subtype-specific therapy.

SLC25A37 as a novel therapeutic target for benign prostatic hyperplasia: integrative analyses of single-cell RNA sequencing and genome-wide association studies.

Hypoxia-associated genes as predictors of outcomes in gastric cancer: a genomic approach.

Integrating single-cell and bulk transcriptomes identifies B cell features associated with neoadjuvant chemoradiotherapy sensitivity in rectal cancer.

Deciphering the Immune Microenvironment at the Forefront of Tumor Aggressiveness by Constructing a Regulatory Network with Single-Cell and Spatial Transcriptomic Data.