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 3k

System / cell line: gene ✕ Clear

Isolated populations and complex disease gene identification.

PMID 18771588 · PMC2575505 · Genome biology · 2008 · 8 claims · 5 setups

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Isolated/founder populations are useful for identifying genes underlying common complex diseases, not just rare monogenic diseases.

genetically icelandic finnish hutterites linkage genome-wide
Design and analysis issues in genome-wide somatic mutation studies of cancer.

PMID 18692126 · PMC2820387 · Genomics · 2009 · 6 claims · 4 setups

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Two-stage (discovery + validation) sequencing designs efficiently allocate resources and can produce highly informative candidate driver gene lists even with relatively small sample sizes.

hypothetical panel colorectal germline simulation targeted genome-wide
Genetic variation of St. Louis encephalitis virus.

PMID 18632961 · PMC2696384 · The Journal of general virology · 2008 · 8 claims · 4 setups

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Phylogenetic analysis of 106 SLEV E gene sequences confirms seven major lineages (I-VII) and refines them into 13 clades (IA, IB, IIA, IIB, IIC, IID, IIG, III, IV, VA, VB, VI, VII)

slev rt-pcr phylogenetic recombination
Development of functional genomic tools in trematodes: RNA interference and luciferase reporter gene activity in Fasciola hepatica.

PMID 18612418 · PMC2440534 · PLoS neglected tropical diseases · 2008 · 8 claims · 8 setups

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Developed a firefly luciferase (fLUC) reporter gene assay to test for the presence of a viable RNAi pathway in helminth parasites

fasciola schistosoma electroporation-mediated rnai whole-mount
Genetic and biochemical studies in Argentinean patients with variegate porphyria.

PMID 18570668 · PMC2467414 · BMC medical genetics · 2008 · 8 claims · 6 setups

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All 18 studied VP patients harbored PPOX gene mutations in heterozygous state

peripheral blood relative urine pcr rt-pcr enzyme
Genome-wide survey of allele-specific splicing in humans.

PMID 18518984 · PMC2427040 · BMC genomics · 2008 · 8 claims · 5 setups

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A genome-wide computational scan identified 30,977 SNPs located within predicted splicing regulatory sequences (donor sites, acceptor sites, branch points, and ESEs)

genome cdna hapmap computational est exon
DiRE: identifying distant regulatory elements of co-expressed genes.

PMID 18487623 · PMC2447744 · Nucleic acids research · 2008 · 8 claims · 4 setups

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DiRE predicts distant regulatory elements by combining gene co-expression data, comparative genomics and TFBS profiles to determine TFBS-association signatures

liver myod transgenic microarray tfbs enhancer
Variation in the Neisseria lactamica porin, and its relationship to meningococcal PorB.

PMID 18451061 · PMC2885628 · Microbiology (Reading, England) · 2008 · 8 claims · 6 setups

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N. lactamica por is less diverse than meningococcal porB2 and porB3

lactamica unique pcr distance-based population
A statistical framework for consolidating "sibling" probe sets for Affymetrix GeneChip data.

PMID 18435860 · PMC2397416 · BMC genomics · 2008 · 7 claims · 4 setups

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A two-way ANOVA model with a treatment x probe-set interaction term can automatically determine whether sibling probe sets for a gene behave similarly (non-significant interaction, consolidate) or differently (significant interaction, treat as independent)

retina thyroid spermatogonial differentially two-way paired anova-based
Variants in the estrogen receptor alpha gene and its mRNA contribute to risk for schizophrenia.

PMID 18424448 · PMC2465798 · Human molecular genetics · 2008 · 8 claims · 8 setups

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Genotype CC (rs2234693/PvuII) and C-allele-containing haplotypes in ESR1 intron 1 are more frequent in African American schizophrenics than controls

genomic postmortem nimhgi esr1 targeted case-control family-based
N-acetyltransferase 8, a positional candidate for blood pressure and renal regulation: resequencing, association and in silico study.

PMID 18402670 · PMC2330028 · BMC medical genetics · 2008 · 7 claims · 6 setups

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NAT8 is a novel positional candidate gene for blood pressure and renal function based on its chromosomal location within a BP linkage region and its expression in embryonic/adult kidney and liver

random reference healthy long-term resequencing quantitative sequence
GPCR genes are preferentially retained after whole genome duplication.

PMID 18382678 · PMC2270905 · PloS one · 2008 · 8 claims · 6 setups

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WGD-derived nGPCR duplicates in Tetraodon nigroviridis are retained at a significantly higher rate (23.5%) than the genome-wide average (15%)

vertebrate ngpcr nigroviridis syntenic phylogenetic chromosomal
Aryl hydrocarbon receptor nuclear translocator (ARNT) gene as a positional and functional candidate for type 2 diabetes and prediabetic intermediate traits: Mutation detection, case-control studies, and gene expression analysis.

PMID 18366646 · PMC2323364 · BMC medical genetics · 2008 · 7 claims · 8 setups

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Common ARNT variants are not associated with type 2 diabetes in European American or African American case-control cohorts

european african individuals nondiabetic snp variant direct
Mutation analysis of the MDM4 gene in German breast cancer patients.

PMID 18279506 · PMC2259322 · BMC cancer · 2008 · 8 claims · 8 setups

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Resequencing of the whole MDM4 coding region in 40 German familial breast cancer patients uncovered two coding variants (V74V and D153G) in 4/40 patients

german bilateral mdm4 lymphoid direct rflp-based splice
Genome-wide prediction of functional gene-gene interactions inferred from patterns of genetic differentiation in mice and men.

PMID 18270580 · PMC2217631 · PloS one · 2008 · 8 claims · 6 setups

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Pairs of unlinked SNPs showing excess genetic differentiation (LD in mouse RILs, Fst in human populations) beyond what simulations/coalescent models predict by chance represent candidate functionally interacting (epistatic) gene pairs.

bxd simulated subset populations genome-wide simulation genotype-phenotype
DNA sequence variants in the LOXL1 gene are associated with pseudoexfoliation glaucoma in a U.S. clinic-based population with broad ethnic diversity.

PMID 18254956 · PMC2270804 · BMC medical genetics · 2008 · 8 claims · 5 setups

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Three LOXL1 SNPs previously associated with pseudoexfoliation in Nordic populations are significantly associated with pseudoexfoliation syndrome and pseudoexfoliation glaucoma in a U.S. ethnically diverse population

patients randomly cohort pxf taqman direct full-gene
A distinct clinical, neuropsychological and radiological phenotype is associated with progranulin gene mutations in a large UK series.

PMID 18234697 · PMC2577762 · Brain : a journal of neurology · 2008 · 8 claims · 7 setups

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Five different pathogenic GRN mutations (frameshift/premature termination) were identified in 25 affected members of a large UK FTLD cohort, with no whole-gene deletions detected

ftld grn genomic post-mortem clinical volumetric direct
Locus-specific and activity-independent gene repositioning during early tumorigenesis.

PMID 18195100 · PMC2213600 · The Journal of cell biology · 2008 · 7 claims · 6 setups

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The genome undergoes global spatial reorganization during both normal and tumorigenic mammary epithelial differentiation, as shown by reduced nucleolar number.

mcf-10a.b2 immunofluorescence interphase quantitative
The commonly-used DNA probe for diffusely-adherent Escherichia coli cross-reacts with a subset of enteroaggregative E. coli.

PMID 20025771 · PMC2803494 · BMC microbiology · 2009 · 7 claims · 5 setups

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The daaC probe cross-hybridizes with a specific subset of EAEC strains, namely those carrying the aafA gene (AAF/II fimbriae)

coli hep-2 pslm862 eaec colony hep-2 pcr
Clear detection of ADIPOQ locus as the major gene for plasma adiponectin: results of genome-wide association analyses including 4659 European individuals.

PMID 20018283 · PMC2845297 · Atherosclerosis · 2010 · 8 claims · 7 setups

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The ADIPOQ locus is the only major gene locus for plasma adiponectin, reaching genome-wide significance in combined and sex-stratified analyses

population-based cohorts gwa plasma genome-wide replication candidate

Experiments

Isolated populations and complex disease gene identification.

Design and analysis issues in genome-wide somatic mutation studies of cancer.

Genetic variation of St. Louis encephalitis virus.

Development of functional genomic tools in trematodes: RNA interference and luciferase reporter gene activity in Fasciola hepatica.

Genetic and biochemical studies in Argentinean patients with variegate porphyria.

Genome-wide survey of allele-specific splicing in humans.

DiRE: identifying distant regulatory elements of co-expressed genes.

Variation in the Neisseria lactamica porin, and its relationship to meningococcal PorB.

A statistical framework for consolidating "sibling" probe sets for Affymetrix GeneChip data.

Variants in the estrogen receptor alpha gene and its mRNA contribute to risk for schizophrenia.

N-acetyltransferase 8, a positional candidate for blood pressure and renal regulation: resequencing, association and in silico study.

GPCR genes are preferentially retained after whole genome duplication.

Aryl hydrocarbon receptor nuclear translocator (ARNT) gene as a positional and functional candidate for type 2 diabetes and prediabetic intermediate traits: Mutation detection, case-control studies, and gene expression analysis.

Mutation analysis of the MDM4 gene in German breast cancer patients.

Genome-wide prediction of functional gene-gene interactions inferred from patterns of genetic differentiation in mice and men.

DNA sequence variants in the LOXL1 gene are associated with pseudoexfoliation glaucoma in a U.S. clinic-based population with broad ethnic diversity.

A distinct clinical, neuropsychological and radiological phenotype is associated with progranulin gene mutations in a large UK series.

Locus-specific and activity-independent gene repositioning during early tumorigenesis.

The commonly-used DNA probe for diffusely-adherent Escherichia coli cross-reacts with a subset of enteroaggregative E. coli.

Clear detection of ADIPOQ locus as the major gene for plasma adiponectin: results of genome-wide association analyses including 4659 European individuals.