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 30

System / cell line: pathway ✕ Assay: cnv ✕ Clear

Single-Cell Transcriptomic Landscape of Right-Sided Colon Cancer Reveals Cellular and Molecular Features of Metastatic Potential.

PMID 41898210 · PMC13024220 · Biomedicines · 2026 · 8 claims · 6 setups

Has reproduction · 71

RCC_LM tumors exhibit higher genomic instability (CNV score) than RCC_noM tumors

right-sided malignant epithelial types scrna-seq copy trajectory
Integrative multi-omics analysis identifies C-type lectin CNVs as functional targets for breeding mastitis-resistant dairy goats.

PMID 41935313 · PMC13188593 · Animal microbiome · 2026 · 8 claims · 8 setups

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Genome-wide CNV scanning of dairy vs non-dairy goats identified 62,860 CNVs, with 115 under strong selection (top 1% Fst/Vst).

goat gmecs lps-induced whole-genome immunofluorescence lentiviral
Single-cell omics data-driven decoding of tumor clonal evolution through reinforcement learning.

PMID 41998716 · PMC13224513 · Genome medicine · 2026 · 8 claims · 3 setups

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scRevol is an RL-based model that infers tumor clonal evolution from scRNA-seq-derived CNV profiles via a label assignment learning strategy.

simulated lineage ovarian scrna-seq-derived
Gene Dosage Analysis on the Single-Cell Transcriptomes Linking Cotranslational Protein Targeting to Metastatic Triple-Negative Breast Cancer.

PMID 34577617 · PMC8472593 · Pharmaceuticals (Basel, Switzerland) · 2021 · 8 claims · 7 setups

Has reproduction · 53

A computational framework mapping single-cell Z-score expression to matched patient-level CNV data can identify recurrent, cross-cell-type copy-number-driven expression (dosage) events.

tnbc independent cng-up breast single-cell gene network
Therapeutic Targeting of Oxidative Phosphorylation in Microsatellite Instability-High Gastric Cancer.

PMID 42038020 · PMC13104725 · Journal of Cancer · 2026 · 7 claims · 8 setups

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MSI gastric cancer samples show significantly greater T cell infiltration and a lower proportion of epithelial cells compared to GS samples

gastric epithelial stomach nod-scid single-cell cnv differential
Molecular profiling of breast cancer in native American women reveals distinct genomic and transcriptomic features.

PMID 41844957 · PMC13144316 · NPJ precision oncology · 2026 · 8 claims · 6 setups

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This is the first multi-omics (mutation, CNV, RNA-seq) characterization of breast tumors from Native American women, providing a resource for future studies

breast degs targeted panel-derived whole-transcriptome
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 profiling reveals malignant states and immune landscapes in PCNSL and systemic DLBCL.

PMID 42023148 · PMC13097095 · iScience · 2026 · 8 claims · 8 setups

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PCNSL and sDLBCL contain five distinct malignant B-cell subtypes (B0-B4) with discrete differentiation trajectories

pcnsl malignant bulk sdlbcl scrna-seq infercnv cytotrace2
Differential Gene Expression and Methylation Analysis of Melanoma in TCGA Database to Further Study the Expression Pattern of KYNU in Melanoma.

PMID 35893303 · PMC9329910 · Journal of personalized medicine · 2022 · 8 claims · 8 setups

Has reproduction · 100

Oncogenes MITF, KIT, CDH1, NRAS, AKT1, EGFR, TP53, and CDK4 are elevated while tumor suppressors PTEN, cAMP, and BCL2 are reduced in melanoma

tcga-skcm melanoma-related intradermal keratinocytes rna-seq kegg copy
Research and experimental verification on the mechanisms of cellular senescence in triple-negative breast cancer.

PMID 38435998 · PMC10909353 · PeerJ · 2024 · 8 claims · 8 setups

Has reproduction · 67

TNBC can be classified into three molecular subtypes (clusters 1, 2, 3) based on cellular senescence-related pathway scores

tnbc tcga tcga-tnbc mda-mb-468 scrna-seq ssgsea unsupervised
Multi-Transcriptomic Analysis Reveals That EREG-Driven TME Crosstalk Defines Anti-EGFR Response in Colorectal Cancer.

PMID 42043480 · PMC13115984 · Cancer medicine · 2026 · 8 claims · 8 setups

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EGFRI eligibility (defined by left-sidedness, RAS/BRAF wild-type, MSS) stratifies cancer cell transcriptomic characteristics more strongly than sidedness alone.

crc epcam+ aggregated cancer scrna-seq copy pseudobulk
Metabolic reprogramming and prognostic insights in molecular landscapes driven by glycolysis in ovarian cancer.

PMID 40707588 · PMC12290113 · Scientific reports · 2025 · 7 claims · 8 setups

Has reproduction · 77

457 differentially expressed GRGs were identified between OC and normal ovarian tissue, of which 30 were significantly associated with prognosis

tcga-oc tcga-oc-gse26193 ov_gse154600 iose-80 bulk univariate copy
Single-cell RNA sequencing of adenoid cystic carcinoma of the breast reveals cellular heterogeneity and tumor microenvironment features.

PMID 41761191 · PMC13041279 · BMC medical genomics · 2026 · 8 claims · 7 setups

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H19+ myoepithelial cells (H19+myoEpC) represent the dominant malignant subpopulation in ACCB, characterized by the majority of large-scale CNVs and high expression of oncogenic pathway genes and ligands (e.g., LAMB1, WNT6)

tumor hnacc epithelial accb single-cell scrna-seq copy
A Soft Matrix Microenvironment Promotes Laterally Spreading Tumors via Oxidative Phosphorylation-Dependent Cell Adhesion.

PMID 41833005 · PMC13248847 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 7 claims · 8 setups

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LSTs exhibit a more malignant phenotype than PAs, with higher inferred CNV scores, stronger genetic correlation with colorectal cancer, and downregulation of adhesion molecules

patients bulk colorectal epithelial clinical bulk single-cell
Multi-omics evaluation of cell lines as models for metastatic prostate cancer.

PMID 41876625 · PMC13171877 · Communications biology · 2026 · 8 claims · 8 setups

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Substantial genomic differences exist between metastatic prostate cancer patient samples and prostate cancer cell lines, including hotspot mutations largely absent from cell lines.

prostate metastatic su2c tcga somatic copy bulk
Single-cell profiling reveals distinct populations of tumor-associated macrophages and metastatic tumor cells in breast cancer brain metastasis.

PMID 42034645 · PMC13247122 · Cell death & disease · 2026 · 8 claims · 8 setups

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Single-cell profiling of BCBM identifies 12 tumor-associated macrophage (TAM) subtypes and 5 metastatic tumor cell (MTC) subtypes with distinct transcriptional profiles

brain breast scrna-seq tams scrna-seq bulk copy
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
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
A differential single-cell transcriptome atlas of left-sided and right-sided colorectal cancer.

PMID 41844817 · PMC13111741 · Discover oncology · 2026 · 8 claims · 8 setups

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MTRNR2L8 is markedly upregulated in RCRC tumor cells and is associated with poorer patient survival

crc epithelial rcrc tcga-read scrna-seq copy gene
Dissecting the immunosuppressive microenvironment of LAMA3 + malignant cells and SPP1 + macrophages in esophageal squamous cell carcinoma using single-cell and spatial transcriptomics.

PMID 41845425 · PMC13104401 · Journal of translational medicine · 2026 · 8 claims · 8 setups

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A LAMA3+ epithelial subpopulation (C3) enriched at the invasive tumor front shows strong EMT signatures and is associated with poor prognosis

escc epithelial scrna-seq tcga-escc scrna-seq spatial infercnv

Experiments

Single-Cell Transcriptomic Landscape of Right-Sided Colon Cancer Reveals Cellular and Molecular Features of Metastatic Potential.

Integrative multi-omics analysis identifies C-type lectin CNVs as functional targets for breeding mastitis-resistant dairy goats.

Single-cell omics data-driven decoding of tumor clonal evolution through reinforcement learning.

Gene Dosage Analysis on the Single-Cell Transcriptomes Linking Cotranslational Protein Targeting to Metastatic Triple-Negative Breast Cancer.

Therapeutic Targeting of Oxidative Phosphorylation in Microsatellite Instability-High Gastric Cancer.

Molecular profiling of breast cancer in native American women reveals distinct genomic and transcriptomic features.

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

Single cell profiling reveals malignant states and immune landscapes in PCNSL and systemic DLBCL.

Differential Gene Expression and Methylation Analysis of Melanoma in TCGA Database to Further Study the Expression Pattern of KYNU in Melanoma.

Research and experimental verification on the mechanisms of cellular senescence in triple-negative breast cancer.

Multi-Transcriptomic Analysis Reveals That EREG-Driven TME Crosstalk Defines Anti-EGFR Response in Colorectal Cancer.

Metabolic reprogramming and prognostic insights in molecular landscapes driven by glycolysis in ovarian cancer.

Single-cell RNA sequencing of adenoid cystic carcinoma of the breast reveals cellular heterogeneity and tumor microenvironment features.

A Soft Matrix Microenvironment Promotes Laterally Spreading Tumors via Oxidative Phosphorylation-Dependent Cell Adhesion.

Multi-omics evaluation of cell lines as models for metastatic prostate cancer.

Single-cell profiling reveals distinct populations of tumor-associated macrophages and metastatic tumor cells in breast cancer brain metastasis.

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

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

A differential single-cell transcriptome atlas of left-sided and right-sided colorectal cancer.

Dissecting the immunosuppressive microenvironment of LAMA3 + malignant cells and SPP1 + macrophages in esophageal squamous cell carcinoma using single-cell and spatial transcriptomics.