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).

• 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

• Discovery and validation of molecular patterns and immune characteristics in the peripheral blood of ischemic stroke patients.

  PMID 38650649 · PMC11034498 · PeerJ · 2024 · 8 claims · 8 setups

  Has reproduction · 83

  188 differentially expressed genes (DEGs) between IS and control blood samples were identified and enriched in immune-related biological pathways

  blood degs peripheral hub microarray kegg cibersort

• 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

  Has reproduction · 84

  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

  tcga-brca triple-negative ffpe bulk univariate kaplan-meier

• A proteomic analysis of IVF follicular fluid in women

  PMID 18980758 · PMC3916005 · Fertility and sterility · 2009 · 8 claims · 4 setups

  Full-text index only

  2D-PAGE proteomic evaluation of follicular fluid can identify potential biomarkers distinguishing good versus poor IVF responders in matched patient pairs

  follicular excised clinical polyacrylamide liquid direct

• Positive Relationships between Intraocular Pressure and Thyroid Function in Graves' Ophthalmopathy: A Three-Aspect Evidence Analysis.

  PMID 40992768 · PMC12479196 · Yonsei medical journal · 2025 · 6 claims · 4 setups

  Has reproduction · 68

  Increased thyroid function is a risk factor for elevated IOP in patients with Graves' ophthalmopathy.

  patients nhanes gtex geo retrospective cross-sectional summary-data-based

• Biomarkers of lupus nephritis determined by serial urine proteomics.

  PMID 18596723 · PMC2614389 · Kidney international · 2008 · 7 claims · 6 setups

  Full-text index only

  SELDI-TOF-MS screening of the LMW urine proteome identifies protein ions that are differentially expressed across phases of the lupus nephritis flare cycle (baseline, pre-flare, flare, post-flare)

  low-molecular-weight lmw urine kidney seldi-tof-ms on-chip capillary

• Merger of ayurveda and tissue culture-based functional genomics: inspirations from systems biology.

  PMID 18348714 · PMC2311278 · Journal of translational medicine · 2008 · 8 claims · 8 setups

  Full-text index only

  Crude LASH extract and its purified components (withanone, withaferin A) act through distinct but partially overlapping molecular gene-regulatory networks

  tumor-derived tumor lash gene cytotoxicity sirna ribozyme

• Bioinformatics methods for learning radiation-induced lung inflammation from heterogeneous retrospective and prospective data.

  PMID 19704920 · PMC2688763 · Journal of biomedicine & biotechnology · 2009 · 8 claims · 3 setups

  Full-text index only

  Kernel-based methods (e.g., SVM) can capture nonlinear dose-volume interactions relevant to predicting radiation pneumonitis

  nsclc inoperable blood retrospective prospective 3-way

• 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

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

  PMID 38601155 · PMC11005030 · Frontiers in immunology · 2024 · 7 claims · 6 setups

  Has reproduction · 71

  An 18-gene mitophagy-related prognostic signature was identified by machine learning and used to build a prognostic risk score model for ALS.

  peripheral als lumbar bulk cibersort gsea

• A platelet-related signature for predicting the prognosis and immunotherapy benefit in bladder cancer based on machine learning combinations.

  PMID 39280688 · PMC11399026 · Translational andrology and urology · 2024 · 8 claims · 8 setups

  Has reproduction · 51

  An Enet (alpha=0.4) machine-learning algorithm built from 10 platelet-related genes yields the optimal platelet-related signature (PRS) for bladder cancer prognosis, with average C-index 0.73

  bladder tcga bulk univariate integrative

• Methylation patterns of the nasal epigenome of hospitalized SARS-CoV-2 positive patients reveal insights into molecular mechanisms of COVID-19.

  PMID 40170038 · PMC11963311 · BMC medical genomics · 2025 · 8 claims · 5 setups

  Has reproduction

  The nasal methylome shows differential DNA methylation in intergenic regions and low methylated regions (LMRs), highlighting distal regulatory/enhancer-like elements in COVID-19 gene regulation

  nasal aggregated severe differentially genome methylation differential

• Quantitative epigenetic co-variation in CpG islands and co-regulation of developmental genes.

  PMID 23999385 · PMC6505400 · Scientific reports · 2013 · 8 claims · 8 setups

  Has reproduction · 95

  Four epigenetic modifications (DNA methylation, H3K4me2, H3K4me3, H3K27me3) in mouse CGIs undergo combinatorial variation (co-variation) across ESCs, NPCs and adult brain during neuron differentiation.

  embryonic escs dem-cgis demg methylation chip-seq gene

• The relationship between PLOD1 expression level and glioma prognosis investigated using public databases.

  PMID 34040895 · PMC8127981 · PeerJ · 2021 · 8 claims · 8 setups

  Has reproduction · 79

  PLOD1 mRNA expression is significantly higher in glioma tissue than in normal brain tissue

  glioma gbm cancer gene online genomic

• Integrated Analysis of Multiple Microarrays Based on Raw Data Identified Novel Gene Signatures in Recurrent Implantation Failure.

  PMID 35197930 · PMC8859149 · Frontiers in endocrinology · 2022 · 6 claims · 7 setups

  Has reproduction · 85

  Robust Rank Aggregation (RRA) can integrate DEG lists from multiple independent RIF microarray datasets to identify robust DEGs.

  endometrium integrated robust ppi microarray robust gene

• A urine extracellular vesicle lncRNA classifier for high-grade prostate cancer and increased risk of progression: A multi-center study.

  PMID 37852185 · PMC10591064 · Cell reports. Medicine · 2023 · 8 claims · 8 setups

  Has reproduction · 65

  A 3-lncRNA urine extracellular vesicle classifier (Clnc: AC015987.1, CTD-2589M5.4, RP11-363E6.3) detects high-grade PCa with higher accuracy than PCA3, mpMRI, PCPT-RC 2.0, and ERSPC-RC

  urinary tcga paired urine sequencing lncrna qrt-pcr

• 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

  In HPV-associated HNSCC, the mitophagy process affects tumour development, immune cell infiltration and prognosis.

  tcga-hnscc gse65858 hpv-positive tcga bulk microarray qrt-pcr

• 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

• Identification and validation of a metabolic-related gene risk model predicting the prognosis of lung, colon, and breast cancers.

  PMID 39779736 · PMC11711664 · Scientific reports · 2025 · 8 claims · 8 setups

  Has reproduction · 74

  540 DEGs overlap across breast, colorectal, and lung cancers out of 11,384 DEGs analyzed

  breast colorectal lung common microarray kegg protein-protein

• A gene signature related to programmed cell death to predict immunotherapy response and prognosis in colon adenocarcinoma.

  PMID 39950044 · PMC11823652 · PeerJ · 2025 · 8 claims · 8 setups

  Has reproduction · 73

  COAD patients can be divided into two molecular subtypes (S1, S2) based on 21 prognostic PCD-related genes, with S1 showing worse prognosis and immunosuppressive microenvironment, S2 showing better prognosis and stronger anti-tumor immunity

  coad consensus cibersort mcp-counter