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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DiRE: identifying distant regulatory elements of co-expressed genes.
PMID 18487623 · PMC2447744 · Nucleic acids research · 2008 · 8 claims · 4 setups
DiRE predicts distant regulatory elements by combining gene co-expression data, comparative genomics and TFBS profiles to determine TFBS-association signatures
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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.
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INTERFEROME: the database of interferon regulated genes.
PMID 18996892 · PMC2686605 · Nucleic acids research · 2009 · 8 claims · 6 setups
INTERFEROME is an open-access database integrating IRG expression data with annotation, orthologue sequences from 37 species, tissue expression, and gene regulatory (TFBS) information
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Inference of transcriptional regulation using gene expression data from the bovine and human genomes.
PMID 17683551 · PMC1978505 · BMC genomics · 2007 · 7 claims · 8 setups
Using human reference promoter sequences is a useful approach for studying gene expression regulation in species with limited or non-existing genomic sequence, such as cattle.