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).

Publications 1.3k Datasets 392.5k Experiments 9

System / cell line: genomics ✕ Assay: correlated ✕ Clear

Exploration of the omics evidence landscape: adding qualitative labels to predicted protein-protein interactions.

PMID 17880677 · PMC2375035 · Genome biology · 2007 · 7 claims · 8 setups

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Combining pairs of omics evidence types into two-dimensional 'evidence landscapes' allows regions to be identified that specifically and purely predict either physical or metabolic protein interactions

saccharomyces correlated chip-chip gene
Putting proteins in one place.

PMID 12790144 · PMC1316915 · Environmental health perspectives · 2003 · 8 claims · 7 setups

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Rapamycin inhibits TOR, causing the silencing protein Sir3 to detach from chromatin at stress-response genes, triggering a coordinated multigene stress response that halts cancer cell proliferation

saccharomyces yeast vascular skin chemical chromatin microarray
Identification of the proliferation/differentiation switch in the cellular network of multicellular organisms.

PMID 17166053 · PMC1664705 · PLoS computational biology · 2006 · 8 claims · 8 setups

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Integrating interactome and transcriptome data reveals a pair of transcriptionally anticorrelated network modules (P and D) each comprising hundreds of genes, present across individuals and species.

postmortem genes gene proteins microarray protein-protein hierarchical
Identification of the shared hub gene signatures and molecular mechanisms between HIV-1 and pulmonary arterial hypertension.

PMID 38528047 · PMC10963360 · Scientific reports · 2024 · 6 claims · 8 setups

Has reproduction · 71

109 shared genes were identified between HIV-1- and PAH-associated WGCNA modules

pbmc shared hub pbmcs weighted kegg differential
Horizontal transmission enables flexible associations with locally adapted symbiont strains in deep-sea hydrothermal vent symbioses.

PMID 35349333 · PMC9168483 · Proceedings of the National Academy of Sciences of the United States of America · 2022 · 8 claims · 6 setups

Has reproduction · 66

Host populations of Alviniconcha and Ifremeria are not genetically differentiated across an ~800-km geographic gradient

gill chemosynthetic host epsilon rna-seq-based metagenomic phylogenomic
A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome.

PMID 16670430 · PMC1456330 · Nucleic acids research · 2006 · 8 claims · 7 setups

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Highly-degenerate RE1 sites are significantly enriched in promoters of validated and putative REST target genes compared to control promoters

orthologous randomized high-score promoters pssm-based comparative motif
Sequence variation in the human transcription factor gene POU5F1.

PMID 18254969 · PMC2275747 · BMC genetics · 2008 · 7 claims · 5 setups

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POU5F1 is highly polymorphic, with a higher polymorphism density than most genes

genomic multi-species inferred international resequencing comparative haplotype
Ultraconserved coding regions outside the homeobox of mammalian Hox genes.

PMID 18816392 · PMC2566984 · BMC evolutionary biology · 2008 · 7 claims · 7 setups

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Ultraconserved coding regions (UCRs, ≥120 nt with no synonymous or nonsynonymous substitutions) exist outside the homeobox in mammalian Hox genes

orthologous hox concatenated intronic sliding comparative molecular
Comprehensive analysis of a novel RNA modifications-related model in the prognostic characterization, immune landscape and drug therapy of bladder cancer.

PMID 37124622 · PMC10131083 · Frontiers in genetics · 2023 · 8 claims · 8 setups

Has reproduction · 71

Two distinct RNA modification patterns exist among BCa samples with radically varying clinical outcomes and biological characteristics

meta-geo tcga-blca bca genomics unsupervised lasso weighted

Experiments

Exploration of the omics evidence landscape: adding qualitative labels to predicted protein-protein interactions.

Putting proteins in one place.

Identification of the proliferation/differentiation switch in the cellular network of multicellular organisms.

Identification of the shared hub gene signatures and molecular mechanisms between HIV-1 and pulmonary arterial hypertension.

Horizontal transmission enables flexible associations with locally adapted symbiont strains in deep-sea hydrothermal vent symbioses.

A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome.

Sequence variation in the human transcription factor gene POU5F1.

Ultraconserved coding regions outside the homeobox of mammalian Hox genes.

Comprehensive analysis of a novel RNA modifications-related model in the prognostic characterization, immune landscape and drug therapy of bladder cancer.