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 · 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 · 49
Integrative transcriptomics and single-cell transcriptomics analyses reveal potential biomarkers and mechanisms of action in papillary thyroid carcinoma.
PMID 40520228 · PMC12162626 · Frontiers in genetics · 2025 · 8 claims · 8 setups
ENTPD1, SERPINA1, and TACSTD2 are potential transcriptomic biomarkers for PTC
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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 · 45
NUSAP1 Could be a Potential Target for Preventing NAFLD Progression to Liver Cancer.
PMID 35431924 · PMC9010788 · Frontiers in pharmacology · 2022 · 8 claims · 8 setups
NUSAP1 is a hub gene linking NAFLD fibrosis progression and HCC and may be a therapeutic target to prevent NAFLD progression to liver cancer
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Has reproduction · 82
SMAGEXP: a galaxy tool suite for transcriptomics data meta-analysis.
PMID 30698691 · PMC6354025 · GigaScience · 2019 · 8 claims · 5 setups
SMAGEXP integrates the metaMA and metaRNASeq R packages into the Galaxy platform to provide a unified gene expression meta-analysis tool suite
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Has reproduction · 85
Integration of multi-omics and machine learning strategies identifies immune related candidate biomarkers in inflammation-associated hypertrophic cardiomyopathy.
PMID 41080564 · PMC12510942 · Frontiers in immunology · 2025 · 8 claims · 8 setups
Seven key immune-related genes (RNF165, SNCA, SRGN, MARCO, STEAP4, SIGLEC9, TKT) are associated with HCM by intersecting DEGs with MR-identified eQTLs
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Has reproduction · 90
Stemness genes and miR-1247-3p expression associate with clinicopathological parameters and prognosis in lung adenocarcinoma.
PMID 37948380 · PMC10637681 · PloS one · 2023 · 6 claims · 7 setups
Three stem cell-related genes (ORC1L, KIF20A, DLGAP5) are differentially expressed in LUAD and correlate with altered immune infiltration and reduced patient survival.
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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
Caloric Restriction Reprograms Adipose Tissues in Rhesus Monkeys.
PMID 41042069 · PMC12686577 · Aging cell · 2025 · 8 claims · 8 setups
At baseline, SAT and VAT transcriptomes are highly similar, with only ~1% of genes (30 genes, adjusted p<0.05) differentially expressed between depots in Controls
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Has reproduction · 84
The seeker R package: simplified fetching and processing of transcriptome data.
PMID 36389425 · PMC9648347 · PeerJ · 2022 · 8 claims · 4 setups
seeker is an R package that wraps existing tools to fetch and process RNA-seq and microarray data, providing a standard interface, simple parallelization, and detailed logging
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Has reproduction · 53
PulmonDB: a curated lung disease gene expression database.
PMID 31949184 · PMC6965635 · Scientific reports · 2020 · 7 claims · 6 setups
PulmonDB is a curated, web-based relational database (plus R package) integrating microarray and RNA-seq gene expression data with controlled-vocabulary annotation for COPD and IPF.
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Has reproduction · 59
Advances in genomic and pharmacokinetic profiling for clinical stratification of metastatic breast cancer.
PMID 41369820 · PMC12799884 · Discover oncology · 2025 · 8 claims · 8 setups
Key genes AR, AKT1, UBC, CDH1, SMAD3, ROR1, and ROR2 are associated with chemotherapy resistance and poor prognosis in metastatic breast cancer
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Has reproduction · 71
Identification of the shared hub gene signatures and molecular mechanisms between HIV-1 and pulmonary arterial hypertension.
PMID 38528047 · PMC10963360 · Scientific reports · 2024 · 7 claims · 7 setups
HIV-1 and PAH share 109 co-expressed genes primarily enriched in type I interferon (IFN) pathways.
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Has reproduction · 58
Identification of common genetic characteristics of rheumatoid arthritis and major depressive disorder by bioinformatics analysis and machine learning.
PMID 37415981 · PMC10320004 · Frontiers in immunology · 2023 · 7 claims · 8 setups
EAF1, SDCBP and RNF19B are common genetic characteristics (hub genes) shared by RA and MDD
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Has reproduction · 94
iBRIDGE: A Data Integration Method to Identify Inflamed Tumors from Single-cell RNA-Seq Data and Differentiate Cell Type-Specific Markers of Immune-Cell Infiltration.
PMID 37023414 · PMC10236149 · Cancer immunology research · 2023 · 8 claims · 8 setups
Malignant cells cluster by patient in scRNA-seq data while immune and stromal cells cluster by cell type, making malignant cells uniquely suited to carry patient-level inflamed/cold signal
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Has reproduction · 96
A Meta-Analysis of the Effects of Acute Sleep Deprivation on the Cortical Transcriptome in Rodent Models.
PMID 41031900 · PMC13131251 · Journal of sleep research · 2026 · 7 claims · 6 setups
Meta-analysis of 18 SD-vs-control contrasts identified 182 genes differentially expressed in the murine cortex in response to sleep deprivation (FDR < 0.05).