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 21

System / cell line: immune ✕ Assay: pan-cancer ✕ Clear

Expression Patterns of Immune Genes Reveal Heterogeneous Subtypes of High-Risk Neuroblastoma.

PMID 32629858 · PMC7408437 · Cancers · 2020 · 8 claims · 8 setups

Has reproduction · 73

Unsupervised biclustering of 283 NB-specific immune genes stratifies HR-NB into two reproducible subtypes: ultra-high-risk (UHR-NB) and (revised) HR-NB.

pediatric target cohorts neuroblastoma bulk spectral kaplan-meier
AGPAT3 reshapes tumor cell vulnerability to IFNγ-mediated ferroptosis and enhances immunotherapy efficacy through lipid remodeling.

PMID 41807033 · PMC12983827 · Journal for immunotherapy of cancer · 2026 · 8 claims · 8 setups

Full-text index only

A ferroptosis-driver gene signature (FD.sig) and machine learning model (FD.model) can predict ICI response

pan-cancer tcga a375 machine single-cell bulk
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

Full-text index only

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
Constructing an APOBEC-related gene signature with predictive value in the overall survival and therapeutic sensitivity in lung adenocarcinoma.

PMID 37954334 · PMC10637964 · Heliyon · 2023 · 8 claims · 8 setups

Has reproduction · 88

APOBEC family genes are differentially expressed across cancer types and tissues, with APOBEC3B being the most aberrantly upregulated gene in most cancers including LUAD

tcga tcga-luad beas-2b rna-seq somatic gene
A pan-cancer single cell landscape reveals heterogeneity and functional diversity of double-negative T cells.

PMID 41484771 · PMC12882460 · Molecular cancer · 2026 · 7 claims · 5 setups

Full-text index only

Integration of pan-cancer scRNA-seq data yields a comprehensive single-cell atlas of 157,025 high-quality DNT cells across 23 cancer types.

tumor dnt ffpe mc38 scrna-seq tcr multiplex
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

Has reproduction · 58

PPARA, PPARD and PPARG are more abnormally expressed in STAD samples and cell lines compared to most of 32 cancer types in TCGA

cancer tcga-stad stomach ges1 rna-seq pearson gsva
Deubiquitination enzyme USP35 negatively regulates MAVS signaling to inhibit anti-tumor immunity.

PMID 40016186 · PMC11868397 · Cell death & disease · 2025 · 8 claims · 8 setups

Has reproduction · 81

USP35 interacts with MAVS and removes its K63-linked polyubiquitin chains, inhibiting viral-induced MAVS-TBK1-IRF3 activation and downstream inflammatory gene expression

tumor melanoma tcga-skcm hek293t bioinformatics geo kaplan-meier
CLK1 Promotes Myeloid-Derived Suppressor Cell Trafficking and Reprograms the Tumor Microenvironment by Activating Hippo/YAP Signaling in Colorectal Cancer.

PMID 41686262 · PMC13136879 · Cancer immunology research · 2026 · 8 claims · 8 setups

Full-text index only

CLK1 is markedly upregulated in immune-cold colorectal tumors and correlates with increased MDSC infiltration and CD8+ T-cell exclusion

colorectal tcga-coad ct26 tumor scrna-seq bulk multiplex
TiRank prioritizes phenotypic niches in tumor microenvironment for clinical biomarker discovery.

PMID 41689080 · PMC12910759 · Genome medicine · 2026 · 7 claims · 4 setups

Full-text index only

TiRank is a framework that integrates scRNA-seq, ST, and bulk transcriptomes using an REO-transformation module and multitask transfer learning to align data into a unified embedding space for prioritizing clinically relevant spatial niches

benchmark pan-cancer gastric independent scrna-seq bulk spatial
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 · 8 claims · 8 setups

Has reproduction · 48

A colon cancer subtype with CD8Ahigh IDO1high tumors shows the worst survival despite high CD8 T cell infiltrates

tcga-coad ncbi-geo tisidb gepia rna-seq tumor-infiltrating gene
A longitudinal, multi-omic atlas reveals the emergence of a spatially organized immunosuppressive ecosystem in resistant melanoma.

PMID 41916292 · PMC13130630 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

Full-text index only

Resistant tumors undergo convergent evolution toward a shared, spatially organized immunosuppressive ecosystem despite genetic heterogeneity.

longitudinal rois tumor exome rna-seq nanostring
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

Full-text index only

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
Colorectal microenvironment determines the prognosis of colorectal cancer.

PMID 41495419 · PMC12868731 · Experimental & molecular medicine · 2026 · 8 claims · 7 setups

Full-text index only

The colorectal microenvironment (classified via NBT gene expression as tumor-supportive vs healthy) can serve as a prognostic biomarker predicting cancer invasiveness and recurrence

paired nbt slide bulk bulk 16s single-cell
Multimodal profiling of pancreatic cancer reveals a TIMP-1-dominated secretory profile determining pro-tumor immunoinstruction in human cancers.

PMID 41564862 · PMC12866174 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

Full-text index only

A 19-factor cancer-immunoinstructive secretory signature (CISS) is present across multiple human cancers and correlates with pro-tumorigenic tumor microenvironments and poor patient survival.

pancreatic kpc pdac tcga-paad rna-seq bulk proteomics
Identification and Validation of an Autophagy-Related Gene Signature for Prognostic Prediction and Immunotherapy Response in Esophageal Squamous Cell Carcinoma.

PMID 41681864 · PMC12897147 · Cancers · 2026 · 8 claims · 8 setups

Full-text index only

A 4-ARG prognostic model (NBEA, CLOCK, NLRX1, MAGEA3) built via stepwise multivariate Cox regression stratifies ESCC patients into high- and low-risk groups with significantly different survival.

escc gse53625 gse160269 imvigor210 microarray univariate single-cell
Multimodal framework for the joint analysis of single-cell RNA and T cell receptor sequencing data predicts T cell response to cancer immunotherapy.

PMID 41820396 · PMC13121706 · Nature communications · 2026 · 8 claims · 7 setups

Full-text index only

TRIM, a conditional multi-modal variational autoencoder integrating paired scRNAseq and scTCRseq data, predicts T cell clonality and transcriptional states at unmeasured tissue sites/timepoints.

hnscc colorectal pan-cancer tcr paired umap convolutional
Helicobacter pylori-linked gene CFAP73 rewires epithelial programs and shapes the gastric cancer microenvironment.

PMID 41934579 · PMC13199538 · Discover oncology · 2026 · 8 claims · 8 setups

Full-text index only

CFAP73 is progressively downregulated during HP infection and is the top-ranked predictor among nine HP-suppressed genes associated with favorable gastric cancer survival

gastric tcga-stad tcga t-cell–tumor jonckheere-terpstra survival random
Identification and verification of diagnostic biomarkers in recurrent pregnancy loss via machine learning algorithm and WGCNA.

PMID 37691920 · PMC10485775 · Frontiers in immunology · 2023 · 8 claims · 8 setups

Has reproduction · 55

352 DEGs (198 up-regulated, 154 down-regulated) were identified between RPL and control endometrial samples

endometrial degs hub decidua microarray wgcna machine
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 · 8 claims · 8 setups

Has reproduction · 71

AML cases can be categorized into two distinct PANRG (PANoptosis-related gene) clusters with differentially expressed prognostic genes (PRDEGs)

aml hovon cancer tcga bulk consensus machine
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

Full-text index only

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

Experiments

Expression Patterns of Immune Genes Reveal Heterogeneous Subtypes of High-Risk Neuroblastoma.

AGPAT3 reshapes tumor cell vulnerability to IFNγ-mediated ferroptosis and enhances immunotherapy efficacy through lipid remodeling.

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

Constructing an APOBEC-related gene signature with predictive value in the overall survival and therapeutic sensitivity in lung adenocarcinoma.

A pan-cancer single cell landscape reveals heterogeneity and functional diversity of double-negative T cells.

Comprehensive analysis of peroxisome proliferator-activated receptors to predict the drug resistance, immune microenvironment, and prognosis in stomach adenocarcinomas.

Deubiquitination enzyme USP35 negatively regulates MAVS signaling to inhibit anti-tumor immunity.

CLK1 Promotes Myeloid-Derived Suppressor Cell Trafficking and Reprograms the Tumor Microenvironment by Activating Hippo/YAP Signaling in Colorectal Cancer.

TiRank prioritizes phenotypic niches in tumor microenvironment for clinical biomarker discovery.

Indoleamine 2, 3-Dioxygenase 1 and CD8 Expression Profiling Revealed an Immunological Subtype of Colon Cancer With a Poor Prognosis.

A longitudinal, multi-omic atlas reveals the emergence of a spatially organized immunosuppressive ecosystem in resistant melanoma.

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

Colorectal microenvironment determines the prognosis of colorectal cancer.

Multimodal profiling of pancreatic cancer reveals a TIMP-1-dominated secretory profile determining pro-tumor immunoinstruction in human cancers.

Identification and Validation of an Autophagy-Related Gene Signature for Prognostic Prediction and Immunotherapy Response in Esophageal Squamous Cell Carcinoma.

Multimodal framework for the joint analysis of single-cell RNA and T cell receptor sequencing data predicts T cell response to cancer immunotherapy.

Helicobacter pylori-linked gene CFAP73 rewires epithelial programs and shapes the gastric cancer microenvironment.

Identification and verification of diagnostic biomarkers in recurrent pregnancy loss via machine learning algorithm and WGCNA.

Machine Learning-Based Integrated Analysis of PANoptosis Patterns in Acute Myeloid Leukemia Reveals a Signature Predicting Survival and Immunotherapy.

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