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 60

System / cell line: prognostic ✕ Assay: analysis ✕ Clear

Multi-omics analyses related to mitochondria and ageing in triple-negative breast cancer implicate PYCR1 potentiates tumor progression.

PMID 41749247 · PMC13041056 · Cancer cell international · 2026 · 8 claims · 8 setups

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A 4-gene mitochondrial ageing-related risk score (MARS) model (PYCR1, MAPT, CEBPA, BCL2A1) predicts TNBC prognosis

tcga-brca gse58812 gse18728 metabric bulk single-cell immunohistochemistry
AI-assisted discovery of an ethnicity-influenced driver of cell transformation in esophageal and gastroesophageal junction adenocarcinomas.

PMID 36134663 · PMC9675486 · JCI insight · 2022 · 8 claims · 8 setups

Has reproduction · 84

An AI-guided Boolean network approach (BoNE) models transcriptomic continuum states of normal esophagus, BE, and EAC to derive classifier gene signatures

gene keratinocyte-derived ffpe spt6-depleted boolean rna-seq immunohistochemistry
Multi-omics analyses related to unfolded protein response in prostate cancer implicate pro-tumor role of IFRD1.

PMID 41694360 · PMC12894258 · Frontiers in immunology · 2026 · 8 claims · 8 setups

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Luminal prostate epithelial cells, especially the LE-KLK3 subpopulation, show elevated UPR activity compared to other cell types

pca tcga-prad external scrna-seq bulk immune
Identification of a novel lncRNA prognostic signature and analysis of functional lncRNA AC115619.1 in hepatocellular carcinoma.

PMID 37614318 · PMC10442647 · Frontiers in pharmacology · 2023 · 8 claims · 8 setups

Has reproduction · 87

A six-lncRNA prognostic signature (LINC02428, LINC02163, AC008549.1, AC115619.1, CASC9, LINC02362) predicts overall survival in HCC patients

hcc tcga paired snu-449 lncrna sequencing univariate
Shared patterns of dysregulated gene expression across squamous cell carcinomas unveil predictors for prognosis and drug sensitivity.

PMID 41803163 · PMC13096486 · Scientific reports · 2026 · 8 claims · 6 setups

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SCCs from head and neck (HNSC), esophagus (ESCC), and cervix (CESC) share highly similar dysregulated gene expression patterns (DGEPs), whereas lung (LUSC) and skin (CSCC) SCCs are more molecularly distinct

tumor combined tcga differential sequencing weighted
Developing a novel immune infiltration-associated mitophagy prediction model for amyotrophic lateral sclerosis using bioinformatics strategies.

PMID 38601155 · PMC11005030 · Frontiers in immunology · 2024 · 8 claims · 8 setups

Has reproduction · 71

Mitophagy-related genes associated with immune infiltration have diagnostic/prognostic significance in ALS

blood als microarray spearman univariate
Comprehensive analysis of a novel RNA modifications-related model in the prognostic characterization, immune landscape and drug therapy of bladder cancer.

PMID 37124622 · PMC10131083 · Frontiers in genetics · 2023 · 8 claims · 8 setups

Has reproduction · 71

Two distinct RNA modification patterns exist among BCa samples with radically varying clinical outcomes and biological characteristics

meta-geo tcga-blca bca genomics unsupervised lasso weighted
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
Integrating single-cell and bulk transcriptomes to reveal prognostic and immunological features of ecDNA-related genes in osteosarcoma.

PMID 42047819 · PMC13125642 · Cancer immunology, immunotherapy : CII · 2026 · 7 claims · 8 setups

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A novel ecDNA-related Gene Prognostic Score Model (EGPSM) was constructed using an integrated framework of 101 machine learning algorithm combinations and validated in training, testing, and external cohorts.

osteosarcoma treatment-naive bulk 143b bulk single-cell cibersort
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
Identification and validation of lymphangiogenesis-related genes for predicting acute myeloid leukemia prognosis: insights from bulk RNA sequencing and single-cell RNA sequencing analyses.

PMID 41772327 · PMC12979290 · Clinical and experimental medicine · 2026 · 7 claims · 8 setups

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A 6-LYMRG risk model (ANGPT1, HGF, MAPK8, PCNA, TBL1XR1, TLR4) is the optimal prognostic signature for AML

gse142698 tcga-laml tcga-laml1 gse116256 differential univariate kaplan-meier
Prognostic significance of p53 and ras gene abnormalities in lung adenocarcinoma patients with stage I disease after curative resection.

PMID 7852188 · PMC5919395 · Japanese journal of cancer research : Gann · 1994 · 6 claims · 5 setups

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Presence of p53 gene abnormalities is associated with shorter disease-free survival in stage I lung adenocarcinoma

formalin-fixed stage pcr-dgge immunohistochemistry pcr-rflp
Cardiovascular genetic medicine: genomic assessment of prognosis and diagnosis in patients with cardiomyopathy and heart failure.

PMID 20559924 · PMC4745893 · Journal of cardiovascular translational research · 2008 · 8 claims · 6 setups

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Molecular signature analysis (MSA) uses machine-learning/classification methods (e.g., PAM/nearest shrunken centroids) on gene expression patterns to classify samples by phenotype for diagnosis, prognosis, or therapy response.

myocardial endomyocardial peripheral pbmcs microarray allomap gene
Identify GDPD3 as a key regulator of epithelial-mesenchymal transition and prostate adenocarcinoma progression via the LPA/LPAR1/AKT axis: transcriptomic and experimental study.

PMID 41562071 · PMC12813044 · Frontiers in immunology · 2025 · 7 claims · 8 setups

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GDPD3 is upregulated in PRAD tumor tissue and its knockdown inhibits tumor cell proliferation, invasion, and migration

prad tcga-prad du145 scrna-seq bulk wgcna
Machine learning-driven transcriptomic and single-cell profiling of programed cell death patterns in colon cancer.

PMID 41854308 · PMC13009810 · Science progress · 2026 · 8 claims · 8 setups

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Disulfidptosis and anoikis are consistently identified as the most robust prognostic PCD patterns in colon cancer across six independent machine learning algorithms

colon coad ssgsea-based machine differential
Metabolic reprogramming of tumor-associated macrophage clusters in ovarian cancer: a single-cell transcriptomic analysis and prognostic model.

PMID 41933362 · PMC13173987 · BioData mining · 2026 · 8 claims · 7 setups

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Single-cell analysis of integrated ovarian cancer datasets identifies 9 distinct mononuclear phagocyte clusters (MPC1-MPC9), of which MPC3, MPC5, and MPC7 are hypermetabolic

ovarian mpc annotated tcga-oc single-cell gene pseudotime
Comprehensive analysis of mitophagy in HPV-related head and neck squamous cell carcinoma.

PMID 37161060 · PMC10170109 · Scientific reports · 2023 · 8 claims · 8 setups

Has reproduction · 73

Mitophagy affects tumour development, immune cell infiltration, and prognosis in HPV-associated HNSCC

hnscc hpv-positive combined rna-seq microarray qrt-pcr
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
Chromosome alterations and E-cadherin gene mutations in human lobular breast cancer.

PMID 10584868 · PMC2374316 · British journal of cancer · 1999 · 8 claims · 5 setups

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LOH at chromosome 16q21-q22.1 occurs in 100% of informative lobular breast tumours, the highest frequency of any region tested

lobular pcr loh loh pcr-sscp sequencing
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

Experiments

Multi-omics analyses related to mitochondria and ageing in triple-negative breast cancer implicate PYCR1 potentiates tumor progression.

AI-assisted discovery of an ethnicity-influenced driver of cell transformation in esophageal and gastroesophageal junction adenocarcinomas.

Multi-omics analyses related to unfolded protein response in prostate cancer implicate pro-tumor role of IFRD1.

Identification of a novel lncRNA prognostic signature and analysis of functional lncRNA AC115619.1 in hepatocellular carcinoma.

Shared patterns of dysregulated gene expression across squamous cell carcinomas unveil predictors for prognosis and drug sensitivity.

Developing a novel immune infiltration-associated mitophagy prediction model for amyotrophic lateral sclerosis using bioinformatics strategies.

Comprehensive analysis of a novel RNA modifications-related model in the prognostic characterization, immune landscape and drug therapy of bladder cancer.

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

Integrating single-cell and bulk transcriptomes to reveal prognostic and immunological features of ecDNA-related genes in osteosarcoma.

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

Identification and validation of lymphangiogenesis-related genes for predicting acute myeloid leukemia prognosis: insights from bulk RNA sequencing and single-cell RNA sequencing analyses.

Prognostic significance of p53 and ras gene abnormalities in lung adenocarcinoma patients with stage I disease after curative resection.

Cardiovascular genetic medicine: genomic assessment of prognosis and diagnosis in patients with cardiomyopathy and heart failure.

Identify GDPD3 as a key regulator of epithelial-mesenchymal transition and prostate adenocarcinoma progression via the LPA/LPAR1/AKT axis: transcriptomic and experimental study.

Machine learning-driven transcriptomic and single-cell profiling of programed cell death patterns in colon cancer.

Metabolic reprogramming of tumor-associated macrophage clusters in ovarian cancer: a single-cell transcriptomic analysis and prognostic model.

Comprehensive analysis of mitophagy in HPV-related head and neck squamous cell carcinoma.

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

Chromosome alterations and E-cadherin gene mutations in human lobular breast cancer.

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