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 4

System / cell line: input ✕ Assay: orthology ✕ Clear

g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments.

PMID 17478515 · PMC1933153 · Nucleic acids research · 2007 · 8 claims · 5 setups

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g:Profiler integrates four modules (g:Profiler core, g:Convert, g:Orth, g:Sorter) into a single cross-linked web tool for gene list analysis

input 1000-bp microarray organisms functional transcription gene
InParanoid 6: eukaryotic ortholog clusters with inparalogs.

PMID 18055500 · PMC2238924 · Nucleic acids research · 2008 · 8 claims · 3 setups

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InParanoid 6 is an updated eukaryotic ortholog database covering 35 species (34 eukaryotes plus E. coli as outgroup), providing pairwise ortholog clusters with inparalogs for all species pairs.

eukaryotic pairwise average pairwise inparanoid upgma
Gene-disease relationship discovery based on model-driven data integration and database view definition.

PMID 19042916 · PMC2639000 · Bioinformatics (Oxford, England) · 2009 · 8 claims · 4 setups

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Explicit gene–disease relationships can be formulated as candidate gene definitions (e.g., co-localization, dysregulation, functional similarity) that may include intermediary orthologous or interacting genes

acgr disease term-based database case
Inventory and analysis of the protein subunits of the ribonucleases P and MRP provides further evidence of homology between the yeast and human enzymes.

PMID 16998185 · PMC1636426 · Nucleic acids research · 2006 · 8 claims · 6 setups

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Fungal Pop8 is evolutionarily related to the Rpp14/Pop5 protein family, suggesting Pop8 is the fungal orthologue of Rpp14

sequences sequence eukaryotic mrp psi-blast phylogenetic hmm

Experiments

g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments.

InParanoid 6: eukaryotic ortholog clusters with inparalogs.

Gene-disease relationship discovery based on model-driven data integration and database view definition.

Inventory and analysis of the protein subunits of the ribonucleases P and MRP provides further evidence of homology between the yeast and human enzymes.