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).

• Why an integrated view of gene expression studies on hematopoiesis in mouse aging is better than the sum of their parts.

  PMID 38627103 · PMC11586588 · FEBS letters · 2024 · 7 claims · 4 setups

  Has reproduction · 75

  Combining differentially expressed (DE) gene lists from multiple publications into a unified 'aging list' (AL) with citation counts, and deriving a shorter high-confidence 'aging signature' (AS, genes cited in >3 publications, ~200 genes), produces a more reliable and consistent picture of hematopoietic aging than any single study.

  hematopoietic compiled gene bulk single-cell

• Specific signature biomarkers highlight the potential mechanisms of circulating neutrophils in aneurysmal subarachnoid hemorrhage.

  PMID 36438795 · PMC9685413 · Frontiers in pharmacology · 2022 · 8 claims · 8 setups

  Has reproduction · 80

  A neutrophil-related co-expression gene module (blue module) is significantly associated with aSAH occurrence

  peripheral genes overlapping neutrophil-related microarray weighted kegg

• 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

• A four-gene signature from blood to exclude bacterial etiology of lower respiratory tract infection in adults.

  PMID 41285807 · PMC12644739 · Nature communications · 2025 · 8 claims · 8 setups

  Has reproduction · 94

  A 4-gene signature (ITGB4, ITGA7, IFI27, FAM20A) derived from whole blood RNA-seq discriminates any bacterial from nonbacterial ARI with cross-validated AUC = 0.90

  hospitalized adults pediatric blood bulk rna-seq microarray

• Integrative analysis of transcriptomic data reveals a predictive gene signature for chemoradiotherapy response in rectal cancer.

  PMID 41550766 · PMC12803930 · iScience · 2026 · 8 claims · 8 setups

  Has reproduction · 50

  A 186-gene signature predictive of nCRT response was derived from integrating six GEO transcriptomic datasets using machine learning.

  pre-treatment combined larc 186-gene differential machine molecular

• Pathway signatures derived from on-treatment tumor specimens predict response to anti-PD1 blockade in metastatic melanoma.

  PMID 34654806 · PMC8519947 · Nature communications · 2021 · 6 claims · 8 setups

  Has reproduction · 100

  A pathway-based super signature from on-treatment samples (PASS-ON) predicts anti-PD1 response with high accuracy (validation AUC 0.85-0.89, combined AUC 0.88) and outperforms existing signatures across all four datasets.

  metastatic pathway bulk gene elastic-net

• Inflammatory Bone Marrow Mesenchymal Stem Cells in Multiple Myeloma: Transcriptional Signature and In Vitro Modeling.

  PMID 37958322 · PMC10650304 · Cancers · 2023 · 8 claims · 8 setups

  Has reproduction · 50

  A 279-gene 'iMSC signature' is upregulated in BM MSCs from MM patients compared to healthy donors, identified by reanalysis of single-cell RNA-seq data.

  facs-isolated expanded bm-mscs mscs single-cell bulk gene

• 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

• GREIN: An Interactive Web Platform for Re-analyzing GEO RNA-seq Data.

  PMID 31110304 · PMC6527554 · Scientific reports · 2019 · 8 claims · 7 setups

  Has reproduction · 73

  GREIN is a web application providing user-friendly interfaces to manipulate, visualize, and analyze GEO RNA-seq data.

  mcf10a nde&dt hypoxia bulk correlation pca

• Identification of a novel 10 immune-related genes signature as a prognostic biomarker panel for gastric cancer.

  PMID 34382341 · PMC8446556 · Cancer medicine · 2021 · 8 claims · 8 setups

  Has reproduction

  A 10-IRG prognostic signature (BMPR1B, GHR, IL11RA, INHBB, NPR3, OBP2A, PTN, R3HDML, TAC1, TPM2) predicts overall survival in gastric cancer.

  gastric tcga-stad overlapping candidate microarray gene rna-seq

• Machine learning developed an intratumor heterogeneity signature for predicting clinical outcome and immunotherapy benefit in bladder cancer.

  PMID 39100839 · PMC11291408 · Translational andrology and urology · 2024 · 8 claims · 8 setups

  Has reproduction · 40

  An integrative machine learning procedure (10 methods, 101 algorithm combinations) identified an Enet (alpha=0.2)-based intratumor heterogeneity-related signature (IRS) with the highest average C-index (0.69) across TCGA and GEO cohorts

  bladder skin bulk integrative immune

• Proteomics as a tool for biomarker discovery.

  PMID 18057524 · PMC3851415 · Disease markers · 2007 · 8 claims · 7 setups

  Full-text index only

  A useful clinical biomarker must be easily attainable, have adequate sensitivity, have adequate specificity, and lead to patient benefit through intervention

  serum laser ovarian seldi-tof two-dimensional gene

• Filling gaps in PPAR-alpha signaling through comparative nutrigenomics analysis.

  PMID 20003344 · PMC2801700 · BMC genomics · 2009 · 7 claims · 8 setups

  Full-text index only

  Meta-analysis of 16 microarray datasets across human, mouse, rat and yeast identifies 164 genes (MDEGs) consistently differentially expressed in response to high fat diet or PPAR signaling perturbation.

  liver saccharomyces mdeg independent microarray transcription chromosomal

• STAT3-dependent analysis reveals PDK4 as independent predictor of recurrence in prostate cancer.

  PMID 32323921 · PMC7178451 · Molecular systems biology · 2020 · 8 claims · 6 setups

  Has reproduction · 66

  Low STAT3 expression in primary PCa is associated with increased OXPHOS and ribosomal biosynthesis at the transcriptomic level

  prostate bulk weighted reverse

• Exploiting convergent phenotypes to derive a pan-cancer cisplatin response gene expression signature.

  PMID 37076665 · PMC10115855 · NPJ precision oncology · 2023 · 8 claims · 8 setups

  Has reproduction · 50

  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

  epithelial-based tcga gdsc muscle-invasive differential co-expression signature

• Identification of Key Genes in Atherosclerosis by Combined DNA Methylation and miRNA Expression Analyses.

  PMID 35949126 · PMC9682560 · Anatolian journal of cardiology · 2022 · 7 claims · 7 setups

  Full-text index only

  10 key genes (TCF7L2, CACNA1C, NRP1, GABBR2, FANCC, DCK, CCDC88C, TCF12, ABLIM1, PBX1) are regulated by both aberrant DNA methylation and miRNA activity in atherosclerosis

  aorta cardiovascular peripheral blood methylation mirna expression

• An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study.

  PMID 27583132 · PMC4972086 · F1000Research · 2016 · 6 claims · 6 setups

  Has reproduction · 74

  An open-source, reproducible RNA-seq pipeline delivered as an IPython notebook and Docker image can process raw RNA-seq data into interactive PCA/HC plots, enrichment results, and small-molecule predictions with minimal setup overhead

  ipsc-derived same top differentially bulk principal hierarchical

• PulmonDB: a curated lung disease gene expression database.

  PMID 31949184 · PMC6965635 · Scientific reports · 2020 · 7 claims · 6 setups

  Has reproduction · 53

  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.

  lung rna-seq curated gene differential

• Integrative analysis reveals chemokines CCL2 and CXCL5 mediated shear stress-induced aortic dissection formation.

  PMID 38163105 · PMC10757018 · Heliyon · 2024 · 8 claims · 8 setups

  Has reproduction · 75

  Integration of three AD RNA-seq datasets identifies 150 common DEGs (100 down-regulated, 50 up-regulated) enriched for blood vessel morphogenesis, muscle structure/tissue development, and chemotaxis.

  aortic gene computational normalized bulk ppi connectivity

• Reverse Engineering of the Pediatric Sepsis Regulatory Network and Identification of Master Regulators.

  PMID 34680414 · PMC8533457 · Biomedicines · 2021 · 7 claims · 8 setups

  Has reproduction · 67

  A set of 15 TFs was identified as sepsis-specific master regulators of pediatric sepsis, dividing into two non-overlapping clusters.

  blood cd4+ pbmc regulons microarray differential master