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 26

System / cell line: immunotherapy ✕ Assay: rna-seq ✕ Clear

Single-cell analysis highlights the significance of malignant cell IFN/MHC-II for immunotherapy response in head and neck squamous cell carcinoma.

PMID 41923630 · PMC13130666 · Cell reports. Medicine · 2026 · 8 claims · 4 setups

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A malignant cell subset expressing IFN-response and MHC-II genes (IFN/MHC-II) increases in proportion after pembrolizumab treatment and is associated with response

hnscc ffpe syngeneic independent single-cell multiplexed tumor
Interpretable artificial intelligence based on immunoregulation-related genes predicts prognosis and immunotherapy response in lung adenocarcinoma.

PMID 41048340 · PMC12491262 · Frontiers in bioinformatics · 2025 · 8 claims · 8 setups

Has reproduction · 71

IRG expression pattern clusters LUAD patients into groups with significantly different survival outcomes and immune cell infiltration

luad normal bulk wgcna tumor
Integrated spatial transcriptomics and pan-cancer XGBoost modeling uncover spatial drivers of immune exclusion and predict immunotherapy response.

PMID 41925746 · PMC13046951 · Cancer immunology, immunotherapy : CII · 2026 · 8 claims · 8 setups

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A three-step computational framework (ImmCeRNA) identified 6,070 immune-related ceRNA interactions across 27 cancer types by integrating expression correlation and experimental validation data.

cancer pan-cancer single lung bulk database single-cell
A novel oxidative stress-related gene signature as an indicator of prognosis and immunotherapy responses in HNSCC.

PMID 38157249 · PMC10781479 · Aging · 2023 · 7 claims · 8 setups

Has reproduction · 85

Consensus clustering of 74 oxidative stress-related genes identifies three distinct HNSCC molecular subgroups (Cluster1-3) with significantly different overall survival and tumor stage distribution

tcga-hnscc gse41613 gse103322 prjeb23709 bulk single-cell immunohistochemistry
Differential Infiltration of Key Immune T-Cell Populations Across Malignancies Varying by Immunogenic Potential and the Likelihood of Response to Immunotherapy.

PMID 39682743 · PMC11640164 · Cells · 2024 · 8 claims · 5 setups

Has reproduction

Estimated T-cell infiltration differs significantly across melanoma, bladder, ovarian, and pancreatic cancers, tracking known immunogenic potential.

tumor melanoma orien bulk gene kaplan-meier
Holliday junction recognition protein (HJURP) could reflect the clinical outcomes of lung adenocarcinoma patients, and impact the choice of precision therapy.

PMID 39649097 · PMC11621083 · Frontiers in genetics · 2024 · 7 claims · 8 setups

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HJURP is a significant prognostic biomarker in LUAD, with high expression associated with increased risk of overall survival death across four independent cohorts

tcga-luad best brain advanced bulk kaplan-meier pearson
Advancing Prognosis Prediction and Immunotherapy Efficacy in Lung Adenocarcinoma Through Machine Learning: Novel Insights From Anoikis Regulator Patterns in Single-Cell Multiomics.

PMID 41488744 · PMC12764181 · International journal of genomics · 2026 · 8 claims · 8 setups

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Epithelial and endothelial cells show the highest anoikis-enriched scores among LUAD TME cell types, with AT2-like Epi being the most anoikis-related epithelial subpopulation.

luad pan-cancer tumor scrna-seq spatial bulk
Single-cell mitophagy signature-based artificial intelligence model enhances prediction of prognosis and immunotherapy response in non-small-cell lung cancer.

PMID 41851738 · PMC13112628 · Respiratory research · 2026 · 8 claims · 8 setups

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A six-gene MRG panel (FOS, CANX, EIF4G1, CALCOCO2, HSP90AB1, PRKAR1A) was selected via LASSO regression as prognostic markers in NSCLC.

nsclc tcga external immunotherapy single-cell bulk transcriptomic
Identification of Cell Subpopulation-Specific Driver Genes Reveals Ideal Candidates for Renal Cell Carcinoma Immunotherapy.

PMID 42074110 · PMC13115843 · International journal of molecular sciences · 2026 · 8 claims · 8 setups

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25 immune-related candidate driver genes were identified from tumor, myeloid, and lymphoid cell gene regulatory networks (GRNs) using SCENIC and topological Q statistics.

kidney lymphoid rcc tcga-kirc single-cell scenic genome-wide
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
Nested co-expression network analysis identifies compact gene clusters in a black box.

PMID 41934621 · PMC13163169 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 6 setups

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Nested-WGCNA is a two-stage algorithm that identifies coarse-grained modules (CGMs) and then, via core decomposition and renormalization, derives fine-grained modules (FGMs) representing subprocesses within each CGM

tcga-blca tcga-kirc tcga-luad imvigor210 bulk scrna-seq
Identifying Molecular Subtypes and 6-Gene Prognostic Signature Based on Hypoxia for Optimizing Targeted Therapies in Non-Small Cell Lung Cancer.

PMID 35509605 · PMC9058021 · International journal of general medicine · 2022 · 8 claims · 8 setups

Has reproduction · 59

NSCLC samples can be classified into two molecular subtypes (C1 and C2) based on hypoxia-related gene expression via consensus clustering

tcga-nsclc geo bulk microarray unsupervised
Pan-cancer evaluation of regulated cell death to predict overall survival and immune checkpoint inhibitor response.

PMID 38538696 · PMC10973470 · NPJ precision oncology · 2024 · 8 claims · 8 setups

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RCD score, defined as the sum of ssGSEA scores of 18 RCD signatures, quantifies overall RCD signaling in a sample

tcga gtex scrna-seq cancer bulk scrna-seq transcriptomic
Human endogenous retrovirus profiling reveals heterogenous expression in cutaneous melanoma.

PMID 41971443 · PMC13061668 · Frontiers in oncology · 2026 · 7 claims · 8 setups

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HERV expression differs between primary and metastatic cutaneous melanoma

tcga-skcm metastatic normal selected bulk consensus orf
Computational analysis of multi-omics data reveals CXCL10(+) DC-Treg interaction drives immunosuppressive microenvironment in AFP-positive hepatocellular carcinoma.

PMID 41854876 · PMC13038760 · Cellular and molecular life sciences : CMLS · 2026 · 8 claims · 8 setups

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STMN1+ and AFP+ malignant cell subsets are enriched in AFP-positive HCC, while CYP3A4+ malignant cells are enriched in AFP-negative HCC

hcc tcga-lihc scrna-seq immunotherapy single-cell bulk spatial
A curated collection of transcriptome datasets to investigate the molecular mechanisms of immunoglobulin E-mediated atopic diseases.

PMID 31290545 · PMC6616200 · Database : the journal of biological databases and curation · 2019 · 7 claims · 8 setups

Has reproduction · 62

A curated collection of 33 GEO transcriptome datasets (1860 profiles) relevant to IgE-mediated atopic disease was assembled and made available on the Gene Expression Browser (GXB) platform

pbmc bronchial nasal skin gene rna-seq
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
A P4HA2 hypoxia signature derived from single cell atlas stratifies conserved subtypes with prognostic significance in cervical squamous cell carcinoma.

PMID 41559646 · PMC12910786 · BMC cancer · 2026 · 6 claims · 8 setups

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A tumor cell metaprogram (MP7) identified from scRNA-seq of CSCC shows elevated hypoxia, invasion, metastasis, proliferation, and angiogenesis scores compared to other metaprograms.

cscc tcga-cscc mp7 siha single-cell bulk gene
Differential cell signaling testing for cell-cell communication inference from single-cell data by dominoSignal.

PMID 41746282 · PMC12998610 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups

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dominoSignal extends the Domino algorithm to enable statistical testing of differential cell-cell signaling between experimental conditions.

single-cell simulated pdac per-sample single-cell simulation cell-cell
PRDM1+ Malignant Cells Mediate an Immunosuppressive Landscape and Resistance to Neoadjuvant Chemoradiotherapy and Immunotherapy in Esophageal Squamous Cell Carcinoma.

PMID 41556358 · PMC13042517 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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A PRDM1+ malignant epithelial cell subcluster (Epi_C4) is enriched in NMPR patients and is associated with nICRT treatment resistance

locally escc pd-1 kyse-30 single-arm scrna-seq bulk

Experiments

Single-cell analysis highlights the significance of malignant cell IFN/MHC-II for immunotherapy response in head and neck squamous cell carcinoma.

Interpretable artificial intelligence based on immunoregulation-related genes predicts prognosis and immunotherapy response in lung adenocarcinoma.

Integrated spatial transcriptomics and pan-cancer XGBoost modeling uncover spatial drivers of immune exclusion and predict immunotherapy response.

A novel oxidative stress-related gene signature as an indicator of prognosis and immunotherapy responses in HNSCC.

Differential Infiltration of Key Immune T-Cell Populations Across Malignancies Varying by Immunogenic Potential and the Likelihood of Response to Immunotherapy.

Holliday junction recognition protein (HJURP) could reflect the clinical outcomes of lung adenocarcinoma patients, and impact the choice of precision therapy.

Advancing Prognosis Prediction and Immunotherapy Efficacy in Lung Adenocarcinoma Through Machine Learning: Novel Insights From Anoikis Regulator Patterns in Single-Cell Multiomics.

Single-cell mitophagy signature-based artificial intelligence model enhances prediction of prognosis and immunotherapy response in non-small-cell lung cancer.

Identification of Cell Subpopulation-Specific Driver Genes Reveals Ideal Candidates for Renal Cell Carcinoma Immunotherapy.

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

Nested co-expression network analysis identifies compact gene clusters in a black box.

Identifying Molecular Subtypes and 6-Gene Prognostic Signature Based on Hypoxia for Optimizing Targeted Therapies in Non-Small Cell Lung Cancer.

Pan-cancer evaluation of regulated cell death to predict overall survival and immune checkpoint inhibitor response.

Human endogenous retrovirus profiling reveals heterogenous expression in cutaneous melanoma.

Computational analysis of multi-omics data reveals CXCL10(+) DC-Treg interaction drives immunosuppressive microenvironment in AFP-positive hepatocellular carcinoma.

A curated collection of transcriptome datasets to investigate the molecular mechanisms of immunoglobulin E-mediated atopic diseases.

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

A P4HA2 hypoxia signature derived from single cell atlas stratifies conserved subtypes with prognostic significance in cervical squamous cell carcinoma.

Differential cell signaling testing for cell-cell communication inference from single-cell data by dominoSignal.

PRDM1+ Malignant Cells Mediate an Immunosuppressive Landscape and Resistance to Neoadjuvant Chemoradiotherapy and Immunotherapy in Esophageal Squamous Cell Carcinoma.