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
The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site.
PMID 18367472 · PMC2377430 · Nucleic acids research · 2008 · 8 claims · 5 setups
1226 eight-letter DNA words show statistically significant positional preferences relative to the TSS across 7914 human promoter regions
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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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Full-text index only
Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness.
PMID 19895688 · PMC3091318 · Genome biology · 2009 · 8 claims · 6 setups
MacroRNA and lincRNA exons are subject to the same relatively low degree of sequence constraint, contrary to prior reports that lincRNAs are far more conserved
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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.