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).

• Molecular Classification Models for Triple Negative Breast Cancer Subtype Using Machine Learning.

  PMID 34575658 · PMC8472680 · Journal of personalized medicine · 2021 · 7 claims · 4 setups

  Has reproduction · 86

  TNBC can be divided into four gene-expression-defined subtypes: BLIA, BLIS, MES, and LAR

  tnbc unique 719-gene gene term machine

• Identification and analysis of genes associated with epithelial ovarian cancer by integrated bioinformatics methods.

  PMID 34143800 · PMC8213194 · PloS one · 2021 · 8 claims · 7 setups

  Has reproduction · 75

  306 overlapping DEGs (265 up-regulated, 41 down-regulated) were identified from three independent GEO microarray datasets comparing EOC and adjacent normal ovarian tissue

  eoc analysis overlapping pubmed microarray kegg protein-protein

• 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

• Prediction of prognostic signatures in triple-negative breast cancer based on the differential expression analysis via NanoString nCounter immune panel.

  PMID 33138797 · PMC7607642 · BMC cancer · 2020 · 8 claims · 8 setups

  Has reproduction · 72

  edgeR-based DEG selection is more appropriate for feature selection than Elastic Net when sample sizes are small.

  ffpe same nanostring tnbc nanostring immunohistochemistry differential

• 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

• 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

• Screening of Diagnostic Biomarkers and Immune Infiltration Characteristics Linking Rheumatoid Arthritis and Rosacea Based on Bioinformatics Analysis.

  PMID 39104909 · PMC11299729 · Journal of inflammation research · 2024 · 8 claims · 8 setups

  Has reproduction · 48

  277 co-expressed DEGs shared between RA and rosacea are enriched in immune processes and chemokine-mediated signaling pathways

  synovial rosacea co-expressed serum microarray weighted protein-protein

• Identification of intrinsic genes across general hypertension, hypertension with left ventricular remodeling, and uncontrolled hypertension.

  PMID 36277786 · PMC9582241 · Frontiers in cardiovascular medicine · 2022 · 7 claims · 8 setups

  Has reproduction · 73

  FBXW4 and 13 other genes are uniquely enriched in the general hypertension group

  peripheral white four gse75360 microarray gene weighted

• Comprehensive bioinformatics analysis and experimental verification identify mitochondrial gene Dgat2 as a novel therapeutic biomarker for myocardial ischemia-reperfusion.

  PMID 40510478 · PMC12159077 · Frontiers in endocrinology · 2025 · 8 claims · 8 setups

  Has reproduction · 64

  Dgat2 is a hub mitochondria-related differentially expressed gene (MitoDEG) that can serve as a novel biomarker and therapeutic target in MI/RI

  heart degs dgat2 mitodegs microarray kegg protein-protein

• LRP1 as a potential diagnostic and immunomodulatory target in endometriosis: evidence from multi-omics and single-cell analyses.

  PMID 42064072 · PMC13124487 · Frontiers in immunology · 2026 · 8 claims · 8 setups

  Has reproduction · 49

  LRP1 is a hub gene with the highest diagnostic performance among 30 candidate hub genes identified by machine learning

  ectopic geo gse5108 training microarray wgcna machine

• Identification of markers correlating with mitochondrial function in myocardial infarction by bioinformatics.

  PMID 39775580 · PMC11684664 · PloS one · 2024 · 7 claims · 8 setups

  Full-text index only

  MitoDEGs in MI are mainly involved in mitochondrial function and ATP synthesis pathways

  left mus combined heart microarray weighted bulk

• Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to Lead (Pb) stress with next generation sequencing.

  PMID 23840502 · PMC3688795 · PloS one · 2013 · 8 claims · 5 setups

  Has reproduction · 27

  A de novo radish root transcriptome of 68,940 assembled transcripts including 33,337 unigenes was generated, providing the first comprehensive molecular characterization of the radish root response to Pb stress.

  radish assembled rna-seq novo functional

• Gene-Expression Profiling Suggests Impaired Signaling via the Interferon Pathway in Cstb-/- Microglia.

  PMID 27355630 · PMC4927094 · PloS one · 2016 · 8 claims · 8 setups

  Has reproduction · 54

  In Cstb-/- microglia, 184 genes were differentially expressed relative to control, of which 33 were identified by both microarray and RNA-seq.

  analysis microarray rna-seq quantitative

• Steps toward broad-spectrum therapeutics: discovering virulence-associated genes present in diverse human pathogens.

  PMID 19874620 · PMC2774872 · BMC genomics · 2009 · 8 claims · 8 setups

  Full-text index only

  Phylogenetic profiling of protein clusters across pathogen and non-pathogen genomes can identify candidate generic virulence factors

  proteins cdc candidate yersinia all-against-all computational cross-species

• Exploring Gene Expression Patterns in Alzheimer's Disease Using a Human Microarray Data Meta-Analysis.

  PMID 41744654 · PMC12938635 · Biology · 2026 · 7 claims · 7 setups

  Has reproduction · 100

  A meta-analysis of eight microarray studies (10 sub-studies) produced a combined list of 4218 statistically significant DEGs between AD and healthy brain at an adjP cut-off of 0.001

  post-mortem combined sub-studies down-regulated microarray differential statistical

• 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 molecular landscape of sepsis severity in infants: enhanced coagulation, innate immunity, and T cell repression.

  PMID 38817614 · PMC11137207 · Frontiers in immunology · 2024 · 8 claims · 8 setups

  Has reproduction · 50

  Only two of seven published sepsis gene signatures (derived from adult/pediatric/geriatric cohorts) showed good concordance (>80% accuracy) when applied to infant sepsis, showing limited generalizability of non-infant signatures.

  blood merged deg microarray coconut pseudotime

• Genomic expression during human myelopoiesis.

  PMID 17683550 · PMC2045681 · BMC genomics · 2007 · 8 claims · 5 setups

  Full-text index only

  An integrated myelopoiesis expression dataset of 9,425 genes, each mapped to a unique genomic position, was generated from 24 microarray experiments across 8 myeloid cell types.

  myeloid same cd34+ gene microarray unsupervised sam

• Identification and verification of diagnostic biomarkers in recurrent pregnancy loss via machine learning algorithm and WGCNA.

  PMID 37691920 · PMC10485775 · Frontiers in immunology · 2023 · 8 claims · 8 setups

  Has reproduction · 55

  352 DEGs (198 up-regulated, 154 down-regulated) were identified between RPL and control endometrial samples

  endometrial degs hub decidua microarray wgcna machine

• Multi-omics analyses identify mannose phosphate isomerase-centered hypoxia-induced angiogenesis signature in colorectal cancer.

  PMID 41204349 · PMC12595641 · Journal of translational medicine · 2025 · 8 claims · 8 setups

  Has reproduction · 61

  Twelve HIA-related genes were identified that are transcriptionally activated by HIF1A/HIF2A and functionally implicated in angiogenesis in CRC

  hct116 crc tumor chip-seq bulk single