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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Molecular cloning, genomic characterization and over-expression of a novel gene, XRRA1, identified from human colorectal cancer cell HCT116Clone2_XRR and macaque testis.
PMID 12908878 · PMC194569 · BMC genomics · 2003 · 8 claims · 7 setups
XRRA1 is a novel gene down-regulated ~2-fold in XR-resistant HCT116 Clone2_XRR relative to HCT116 Clone10, identified via cDNA microarray
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Identification of direct regulatory targets of the transcription factor Sox10 based on function and conservation.
PMID 18786246 · PMC2556353 · BMC genomics · 2008 · 6 claims · 6 setups
PLP, Sox10, SOD3, and Ptn are direct regulatory targets of Sox10, confirmed by chromatin immunoprecipitation binding to conserved cis-elements
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Predicting survival within the lung cancer histopathological hierarchy using a multi-scale genomic model of development.
PMID 16800721 · PMC1483910 · PLoS medicine · 2006 · 8 claims · 8 setups
Multi-scale genomic similarities exist between four human lung cancer subtypes and the developing mouse lung, and these similarities are prognostically meaningful.
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Has reproduction · 100
Exploring Gene Expression Patterns in Alzheimer's Disease Using a Human Microarray Data Meta-Analysis.
PMID 41744654 · PMC12938635 · Biology · 2026 · 6 claims · 7 setups
AD brains show a distinct transcriptomic profile with up-regulation of immune/inflammation genes and down-regulation of synapse/neuronal-signaling genes
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Are gene expression microarray analyses reliable? A review of studies of retinoic acid responsive genes.
PMID 15626329 · PMC5171945 · Genomics, proteomics & bioinformatics · 2003 · 6 claims · 8 setups
Published microarray studies aiming to identify RA-responsive genes show substantial, often contradictory, differences in results across research groups.
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Application of functional genomics to primate endometrium: insights into biological processes.
PMID 17118168 · PMC1775064 · Reproductive biology and endocrinology : RB&E · 2006 · 8 claims · 7 setups
Gene expression profiles differ distinctly across proliferative, early-, mid-, and late-secretory phases of the human menstrual cycle, reflecting sequential estradiol and progesterone action.
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Effects of DNA-targeted ionizing radiation produced by 5-[125I]iodo-2'-deoxyuridine on global gene expression in primary human cells.
PMID 17594496 · PMC1934370 · BMC genomics · 2007 · 8 claims · 7 setups
125I-IUdR-induced DNA damage alters expression of only a limited subset of genes in primary human cells
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CYCLONET--an integrated database on cell cycle regulation and carcinogenesis.
PMID 17202170 · PMC1899094 · Nucleic acids research · 2007 · 7 claims · 4 setups
Cyclonet is a web-based integrated database combining 'omics' and chemoinformatics data on mammalian cell cycle regulation in normal and pathological (cancer) states, built on a systems biology approach.
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Genomic expression during human myelopoiesis.
PMID 17683550 · PMC2045681 · BMC genomics · 2007 · 8 claims · 5 setups
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.
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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 · 76
PI3K inhibitors protect against glucocorticoid-induced skin atrophy.
PMID 30737086 · PMC6441871 · EBioMedicine · 2019 · 7 claims · 8 setups
PI3K/mTOR/Akt inhibitors are a pharmacological class that represses glucocorticoid-induced REDD1 and FKBP51 expression, identified via LINCS drug-repurposing screen.
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Inferring combinatorial regulation of transcription in silico.
PMID 15647509 · PMC546154 · Nucleic acids research · 2005 · 8 claims · 5 setups
Combining Cluster-Buster (TFBS cluster prediction) with GOSSIP (rigorous GO enrichment statistics with multiple-testing/FDR correction) predicts biological functions controlled by combinatorial transcription factor action, without prior knowledge of factor targets
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Connecting synthetic chemistry decisions to cell and genome biology using small-molecule phenotypic profiling.
PMID 19825513 · PMC2787914 · Current opinion in chemical biology · 2009 · 8 claims · 8 setups
Multidimensional phenotypic profiling leverages information content from multiple parallel or multiplexed measurements of compound action on cells, unlike hierarchical screening which filters to few 'interesting' compounds.
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Current and future directions in genomics of amyotrophic lateral sclerosis.
PMID 18625410 · PMC3524513 · Physical medicine and rehabilitation clinics of North America · 2008 · 8 claims · 8 setups
Familial ALS (FALS, 5-10% of cases) follows Mendelian autosomal dominant inheritance, with 20% caused by SOD1 mutations and 80% by unknown mutations
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Sequencing the regulatory genome.
PMID 18598374 · PMC2481419 · Genome biology · 2008 · 8 claims · 8 setups
Nuclear-lamina-associated domains (LADs) define chromatin regions with distinct transcriptional characteristics (fewer, lower-expressed genes, low RNA Pol II occupancy, H3K27me3-enriched borders)