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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Full-text index only
EPD in its twentieth year: towards complete promoter coverage of selected model organisms.
PMID 16381980 · PMC1347508 · Nucleic acids research · 2006 · 7 claims · 4 setups
EPD is an annotated, non-redundant collection of experimentally defined eukaryotic POL II promoters accessed via genome position pointers.
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Has reproduction · 62
Application of alternative de novo motif recognition models for analysis of structural heterogeneity of transcription factor binding sites: a case study of FOXA2 binding sites.
PMID 34547062 · PMC8408018 · Vavilovskii zhurnal genetiki i selektsii · 2021 · 8 claims · 4 setups
MultiDeNA pipeline combines PWM, diPWM, BaMM and InMoDe models to train, evaluate, threshold, and classify ChIP-seq peaks for TFBS structural heterogeneity
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Full-text index only
ABS: a database of Annotated regulatory Binding Sites from orthologous promoters.
PMID 16381947 · PMC1347478 · Nucleic acids research · 2006 · 7 claims · 6 setups
ABS is a public database of experimentally identified TF binding sites conserved in orthologous vertebrate gene promoters, manually curated from the literature.
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Has reproduction · 49
oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets.
PMID 22973536 · PMC3429929 · G3 (Bethesda, Md.) · 2012 · 8 claims · 6 setups
oPOSSUM-3 is a web-accessible system that identifies over-represented TFBS and TFBS families in DNA sequences of co-expressed genes or in sequences from high-throughput methods such as ChIP-Seq.