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).
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Has reproduction · 76
High DNA methylation age deceleration defines an aggressive phenotype with immunoexclusion environments in endometrial carcinoma.
PMID 37388735 · PMC10303802 · Frontiers in immunology · 2023 · 8 claims · 8 setups
Almost 90% of TCGA EC tumors exhibit DNA methylation age deceleration (DNAmad) relative to patient chronological age as assessed by the Horvath clock
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Has reproduction · 50
Exploiting convergent phenotypes to derive a pan-cancer cisplatin response gene expression signature.
PMID 37076665 · PMC10115855 · NPJ precision oncology · 2023 · 8 claims · 8 setups
A convergent-phenotype-based seed gene/co-expression method can extract consensus gene expression signatures predictive of response to chemotherapeutic drugs in the GDSC database
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Has reproduction · 66
STAT3-dependent analysis reveals PDK4 as independent predictor of recurrence in prostate cancer.
PMID 32323921 · PMC7178451 · Molecular systems biology · 2020 · 6 claims · 4 setups
Low STAT3 expression in primary prostate cancer is associated with up-regulated OXPHOS and ribosomal biosynthesis at the transcriptomic level.
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Has reproduction · 78
Evaluating Distribution and Prognostic Value of New Tumor-Infiltrating Lymphocytes in HCC Based on a scRNA-Seq Study With CIBERSORTx.
PMID 33043022 · PMC7527443 · Frontiers in medicine · 2020 · 5 claims · 6 setups
CIBERSORTx can combine scRNA-seq-derived signatures with bulk HCC transcriptomes to estimate proportions of 11 TIL subsets and infer cell-type-specific gene expression.
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Has reproduction · 91
Exploring the key genetic association between chronic pancreatitis and pancreatic ductal adenocarcinoma through integrated bioinformatics.
PMID 37501719 · PMC10369079 · Frontiers in genetics · 2023 · 6 claims · 7 setups
CEL (carboxyl ester lipase) is the real hub gene shared between CP and PDAC and is markedly downregulated in PDAC
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Has reproduction · 96
Mammary cell gene expression atlas links epithelial cell remodeling events to breast carcinogenesis.
PMID 34079055 · PMC8172904 · Communications biology · 2021 · 8 claims · 8 setups
An integrated 50K mouse and 24K human mammary epithelial cell atlas (scRNA-seq) captures mammary epithelium reorganization across most lifetime stages.
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Has reproduction · 100
Proneural-mesenchymal antagonism dominates the patterns of phenotypic heterogeneity in glioblastoma.
PMID 38433919 · PMC10905000 · iScience · 2024 · 8 claims · 8 setups
The four proposed GBM molecular subtypes (Proneural, Neural, Classical, Mesenchymal / NPC-like, OPC-like, AC-like, MES-like) are not mutually exclusive or independent of one another
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Has reproduction · 48
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 · 7 claims · 6 setups
The CD8A-high/IDO1-high colon cancer subtype (group IV*) has the worst survival despite high CD8 infiltrates.
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Has reproduction · 50
Wx: a neural network-based feature selection algorithm for transcriptomic data.
PMID 31324856 · PMC6642261 · Scientific reports · 2019 · 8 claims · 8 setups
The Wx algorithm ranks genes by a discriminative index (DI) score representing classification power for distinguishing given groups, enabling intuitive selection of optimal biomarker genes.
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Has reproduction · 85
A novel oxidative stress-related gene signature as an indicator of prognosis and immunotherapy responses in HNSCC.
PMID 38157249 · PMC10781479 · Aging · 2023 · 6 claims · 7 setups
A nine-gene oxidative stress-related scoring (OSRS) model (AREG, CES1, CSTA, FDCSP, JCHAIN, IFFO2, PGLYRP4, SPOCK2, SPINK6) predicts overall survival in HNSCC.
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Has reproduction · 32
Developing prognostic gene panel of survival time in lung adenocarcinoma patients using machine learning.
PMID 35117753 · PMC8799101 · Translational cancer research · 2020 · 7 claims · 4 setups
A panel of 22 genetic features with Naïve Bayes can predict whether lung adenocarcinoma patient survival time is >3 years (accuracy=75%, AUC=0.81).
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Has reproduction · 76
Correcting scale distortion in RNA sequencing data.
PMID 39875825 · PMC11776150 · BMC bioinformatics · 2025 · 8 claims · 8 setups
Local averaging reveals expression-level-dependent biases that differ from sample to sample across all RNA-seq datasets studied, and are not corrected by conventional normalization (TPM/FPKM)
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Has reproduction · 71
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
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
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Has reproduction · 88
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
APOBEC family genes are aberrantly expressed across cancers, with APOBEC3B the most consistently upregulated, and APOBEC3B/APOBEC3A are markedly altered in LUAD
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Has reproduction · 59
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
NSCLC samples can be classified into two molecular subtypes (C1 and C2) based on hypoxia-related gene expression via consensus clustering
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Has reproduction · 84
Elucidating the Prognostic and Therapeutic Implications of Insulin Resistance Genes in Breast Cancer: A Machine Learning-Powered Analysis.
PMID 40427728 · PMC12109394 · Biology · 2025 · 8 claims · 8 setups
A seven-gene IRG prognostic signature (LIFR, EZR, TBC1D4, NSF, RPL5, SAA1, PGK1) predicts overall survival in breast cancer across training and four validation cohorts
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Has reproduction · 77
Metabolic reprogramming and prognostic insights in molecular landscapes driven by glycolysis in ovarian cancer.
PMID 40707588 · PMC12290113 · Scientific reports · 2025 · 7 claims · 8 setups
457 differentially expressed GRGs were identified between OC and normal ovarian tissue, of which 30 were significantly associated with prognosis
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Has reproduction · 48
Bioinformatics Analysis of the Characteristics and Correlation of m6A Methylation in Breast Cancer Progression.
PMID 35655723 · PMC9148239 · Contrast media & molecular imaging · 2022 · 8 claims · 8 setups
Breast cancer samples can be divided into 4 m6A subtypes (quiescent, m6A methylation, protein-binding, mixed) based on expression of m6A-related genes, with consistent proportions across datasets
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Has reproduction · 84
DeepProg: an ensemble of deep-learning and machine-learning models for prognosis prediction using multi-omics data.
PMID 34261540 · PMC8281595 · Genome medicine · 2021 · 6 claims · 7 setups
DeepProg, an ensemble of deep-learning and machine-learning models, robustly predicts patient survival subtypes from multi-omics data and explicitly models survival as the objective while predicting new patient risks
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Has reproduction · 73
Comprehensive analysis of mitophagy in HPV-related head and neck squamous cell carcinoma.
PMID 37161060 · PMC10170109 · Scientific reports · 2023 · 8 claims · 8 setups
In HPV-associated HNSCC, the mitophagy process affects tumour development, immune cell infiltration and prognosis.