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 1.6k

System / cell line: genome ✕ Clear

Characterization of genome-wide p53-binding sites upon stress response.

PMID 18474530 · PMC2441782 · Nucleic acids research · 2008 · 7 claims · 7 setups

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Genome-wide ChIP-on-chip identified 1546 high-confidence p53-binding sites upon Actinomycin D treatment in U2OS cells

u2os saos-2 chip-on-chip chip-qpcr western
Genetic and functional association of FAM5C with myocardial infarction.

PMID 18430236 · PMC2383879 · BMC medical genetics · 2008 · 8 claims · 5 setups

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SNPs within FAM5C show genetic linkage to and association with myocardial infarction in the GENECARD family-based sample

genecard cathgen donor aortic genome-wide case-control expression
Comparative genomic analysis of Mycobacterium avium subspecies obtained from multiple host species.

PMID 18366709 · PMC2323391 · BMC genomics · 2008 · 8 claims · 5 setups

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Genome diversity among M. avium subspecies is mediated by large sequence polymorphisms (LSPs) commonly associated with mobile genetic elements.

avium microarray map selected microarray blastn sequencing
Genomics and biology come together to fight HIV.

PMID 18366259 · PMC2270331 · PLoS biology · 2008 · 8 claims · 6 setups

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Genome-wide association studies have identified ~100 genetic polymorphisms robustly (genome-wide significant) linked to common human traits/diseases, but the biological mechanisms behind most remain unknown.

ceph hiv-positive elledge heritability linkage modified
A sequence-based survey of the complex structural organization of tumor genomes.

PMID 18364049 · PMC2397511 · Genome biology · 2008 · 8 claims · 6 setups

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End sequencing profiling (ESP) can identify all classes of genome rearrangements in tumor genomes by paired-end sequencing of BAC clones

tumors breast bac bt474 bac low-coverage fluorescence
A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence.

PMID 18344523 · PMC2377433 · Nucleic acids research · 2008 · 7 claims · 6 setups

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Spaln maps and aligns large cDNA sequence sets onto whole mammalian genomes using substantially less memory than comparable existing tools

unigene shuffled real genomes genome-wide alignment gene
Proteomic view of mitochondrial function.

PMID 18331620 · PMC2374722 · Genome biology · 2008 · 8 claims · 8 setups

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Most modulators of basal mitochondrial function identified in the Drosophila RNAi screen are located outside the mitochondrion, since only 17 of 152 hits had a clear mitochondrial function.

drosophila saccharomyces caenorhabditis yeast genome-wide phenotypic morphology
Sequence context affects the rate of short insertions and deletions in flies and primates.

PMID 18291026 · PMC2374710 · Genome biology · 2008 · 8 claims · 6 setups

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The rate of insertion or deletion of specific lengths can vary by more than 100-fold depending on the surrounding sequence context

chimpanzee simulans chimp primate comparative direct nucleotide
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
Commonality of functional annotation: a method for prioritization of candidate genes from genome-wide linkage studies.

PMID 18263617 · PMC2275105 · Nucleic acids research · 2008 · 8 claims · 7 setups

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Genes correlated with a common complex trait are more likely to share GO functional annotations than genes not correlated with that trait

genes candidate simulated alzheimer's genome-wide term null-hypothesis
Hominoid chromosomal rearrangements on 17q map to complex regions of segmental duplication.

PMID 18257913 · PMC2374708 · Genome biology · 2008 · 8 claims · 7 setups

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The macaque marker order on chromosome 17 represents the ancestral hominoid/mammalian organization

great felis mus rhesus comparative fish duplicon
Mechanisms of disease: genetic insights into the etiology of type 2 diabetes and obesity.

PMID 18212765 · PMC7116808 · Nature clinical practice. Endocrinology & metabolism · 2008 · 8 claims · 8 setups

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Six high-density genome-wide association studies in over 19,000 individuals identified approximately ten T2D-susceptibility loci, including HHEX, IDE, SLC30A8, FTO, CDKAL1, CDKN2A/CDKN2B, and IGF2BP2.

t2d icelandic population tcf7l2 genome-wide linkage candidate-gene
A genome search for primary vesicoureteral reflux shows further evidence for genetic heterogeneity.

PMID 18197425 · PMC2259258 · Pediatric nephrology (Berlin, Germany) · 2008 · 8 claims · 7 setups

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Genome-wide linkage analysis identifies several novel loci for primary VUR on chromosomes 1, 3, 4, and 22, supporting genetic heterogeneity.

patients multiplex index pedigree genome-wide fine-mapping haplotype
Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans.

PMID 18193044 · PMC2682493 · Nature genetics · 2008 · 8 claims · 7 setups

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GWAS plus targeted replication identified 18 loci reproducibly associated with LDL cholesterol, HDL cholesterol, and/or triglycerides, six of which are newly identified

blood liver fasting genome-wide targeted liver
Conserved elements with potential to form polymorphic G-quadruplex structures in the first intron of human genes.

PMID 18187510 · PMC2275096 · Nucleic acids research · 2008 · 8 claims · 6 setups

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G-richness downstream of the TSS is strand-biased, concentrated on the nontemplate strand, with a peak at +200 to +300 bp

refseq chicken random genome-wide quadparser regulatory
Discovery and validation of new molecular targets in treating dyslipidemia: the role of human genetics.

PMID 20211435 · PMC3328807 · Trends in cardiovascular medicine · 2009 · 8 claims · 8 setups

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Mendelian randomization uses genetic variants as a 'randomized trial of nature' to assess causal relationships between lipid biomarkers and CHD, overcoming confounding and reverse causality limitations of observational epidemiology.

population myocardial individuals animal genome-wide case-control gene
Genome-wide association studies of MRI-defined brain infarcts: meta-analysis from the CHARGE Consortium.

PMID 20044523 · PMC2923092 · Stroke · 2010 · 8 claims · 6 setups

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SNP rs2208454 in intron 3 of MACROD2 (near FLRT3, chr20p12) is associated with lower risk of covert MRI-infarcts (OR=0.76, p=4.64x10-7)

stroke-free elderly african-american cardiovascular genome-wide direct expression
TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity.

PMID 25391375 · PMC4315292 · Genome research · 2015 · 8 claims · 8 setups

Has reproduction · 80

TP53 binding events fall into three distinct categories defined by the local chromatin environment: TSS (H3K4me3+), enhancer (H3K4me1+/H3K4me3-), and distal (H3K4me1-/H3K4me3-) peaks.

imr90 hct116 chip-seq rna-seq atac-seq
Mutations in the formin gene INF2 cause focal segmental glomerulosclerosis.

PMID 20023659 · PMC2980844 · Nature genetics · 2010 · 8 claims · 8 setups

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Mutations in INF2, a formin family actin-regulating protein, cause autosomal dominant focal segmental glomerulosclerosis (FSGS)

families genes individuals kidney genome-wide sanger resequencing
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

Characterization of genome-wide p53-binding sites upon stress response.

Genetic and functional association of FAM5C with myocardial infarction.

Comparative genomic analysis of Mycobacterium avium subspecies obtained from multiple host species.

Genomics and biology come together to fight HIV.

A sequence-based survey of the complex structural organization of tumor genomes.

A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence.

Proteomic view of mitochondrial function.

Sequence context affects the rate of short insertions and deletions in flies and primates.

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

Commonality of functional annotation: a method for prioritization of candidate genes from genome-wide linkage studies.

Hominoid chromosomal rearrangements on 17q map to complex regions of segmental duplication.

Mechanisms of disease: genetic insights into the etiology of type 2 diabetes and obesity.

A genome search for primary vesicoureteral reflux shows further evidence for genetic heterogeneity.

Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans.

Conserved elements with potential to form polymorphic G-quadruplex structures in the first intron of human genes.

Discovery and validation of new molecular targets in treating dyslipidemia: the role of human genetics.

Genome-wide association studies of MRI-defined brain infarcts: meta-analysis from the CHARGE Consortium.

TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity.

Mutations in the formin gene INF2 cause focal segmental glomerulosclerosis.

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