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 115

System / cell line: flanking ✕ Assay: genomic ✕ Clear

Comparative genomics and experimental promoter analysis reveal functional liver-specific elements in mammalian hepatic lipase genes.

PMID 17428321 · PMC1853088 · BMC genomics · 2007 · 8 claims · 7 setups

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Cis-regulatory elements responsible for liver-specific HL expression are conserved among mammalian HL genes

5'-flanking upstream transiently genomic comparative tfbs promoter-reporter
Assessing the genomic evidence for conserved transcribed pseudogenes under selection.

PMID 19754956 · PMC2753554 · BMC genomics · 2009 · 8 claims · 8 setups

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1750 transcribed pseudogene annotations (TPAs) were identified in the human genome, ~11.5% of all human pseudogene annotations.

genome rhesus vega-annotated tpas transcript-to-genome same synteny
Genomic profiling of microRNA and messenger RNA reveals deregulated microRNA expression in prostate cancer.

PMID 18676839 · PMC2597340 · Cancer research · 2008 · 8 claims · 7 setups

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MicroRNA processing components (Dicer, DGCR8) and microRNA host genes (MCM7, C9orf5) are significantly up-regulated in prostate tumors versus non-tumor tissue

prostate subset lncap 22rv1 microrna quantitative western
MutScreener: primer design tool for PCR-direct sequencing.

PMID 16845093 · PMC1538803 · Nucleic acids research · 2006 · 8 claims · 4 setups

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MutScreener is a web-based application that automates PCR-direct sequencing assay design by annotating gene structure and designing PCR and sequencing primers.

sim4 cdna gene comparative sequence pcr
Comparative genomic study reveals a transition from TA richness in invertebrates to GC richness in vertebrates at CpG flanking sites: an indication for context-dependent mutagenicity of methylated CpG sites.

PMID 19329065 · PMC5054122 · Genomics, proteomics & bioinformatics · 2008 · 8 claims · 8 setups

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Nucleotide preference at CpG flanking sites transitions from 5' T (invertebrates) to 5' A (vertebrates) at the invertebrate-vertebrate boundary

genomes same pufferfish elegans nucleotide genome-wide kruskal-wallis
Intronic alternative splicing regulators identified by comparative genomics in nematodes.

PMID 16839192 · PMC1500816 · PLoS computational biology · 2006 · 8 claims · 6 setups

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Conserved intronic elements flanking alternative exons occur more often than expected from total intron sequence, consistent with selective pressure for splicing regulation

elegans database transgenic comparative est cross-species
Retinitis pigmentosa: mutation analysis of RHO, PRPF31, RP1, and IMPDH1 genes in patients from India.

PMID 18552984 · PMC2426732 · Molecular vision · 2008 · 8 claims · 4 setups

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Coding/flanking regions of RHO, PRPF31, and IMPDH1, plus exons 4F/4G/4H of RP1, were PCR-amplified and directly sequenced in 48 isolated and 53 adRP Indian patients and 75 controls

genomic peripheral probands identified pcr reverse clinical
Adequate use of allele frequencies in Hispanics--a problem elucidated in nephrotic syndrome.

PMID 19876656 · PMC2899680 · Pediatric nephrology (Berlin, Germany) · 2010 · 7 claims · 3 setups

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Self-identified Hispanic SRNS patients in the USA are genetically heterogeneous, being of either Caucasian or Mesoamerican (Native-American) descent

genomic same healthy direct genome-wide
Two previously proposed P1/P2-differentiating and nine novel polymorphisms at the A4GALT (Pk) locus do not correlate with the presence of the P1 blood group antigen.

PMID 16212661 · PMC1282566 · BMC genetics · 2005 · 8 claims · 4 setups

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The previously proposed P2-specific markers -551_-550insC and -160A>G do not correlate with P1/P2 phenotype, since they occur homozygously in many P1 individuals too

genomic erythrocytes direct pcr pcr-asp
Genetic analysis of three Korean patients with clinical features of Ehlers-Danlos syndrome type IV.

PMID 17728513 · PMC2693823 · Journal of Korean medical science · 2007 · 7 claims · 6 setups

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EDS type IV is genetically heterogeneous; not all clinically/biochemically diagnosed patients carry COL3A1 mutations

genomic peripheral abdominal cerebral direct genomic angiography
In silico comparative genomic analysis of GABAA receptor transcriptional regulation.

PMID 17603907 · PMC1934366 · BMC genomics · 2007 · 8 claims · 8 setups

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Previously unreported putative promoters were identified for the β2, γ1, γ3, ε, θ and π GABA A receptor subunit genes

subunit mammalian α1-β2-γ2-α6 cross-species promoter transcription
Glucokinase gene mutations: structural and genotype-phenotype analyses in MODY children from South Italy.

PMID 18382660 · PMC2270336 · PloS one · 2008 · 8 claims · 6 setups

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16 of 30 patients with suspected MODY (53%) carry GCK mutations, confirming GCK MODY diagnosis

genomic gck fasting pediatric direct molecular biochemical
Single-track sequencing for genotyping of multiple SNPs in the N-acetyltransferase 1 (NAT1) gene.

PMID 15563733 · PMC544357 · BMC biotechnology · 2004 · 8 claims · 6 setups

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A single-track sequencing (SSR) strategy on one PCR product can simultaneously address 24 genetic variants in the NAT1 gene using paired terminator tracks (A/G for coding region, A/T for 3' flanking region)

genomic nat1 same pcr single-track single
Selection of target sites for mobile DNA integration in the human genome.

PMID 17166054 · PMC1664696 · PLoS computational biology · 2006 · 8 claims · 8 setups

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A comprehensive bioinformatic method was developed to annotate every base pair in the human genome for its likelihood of hosting integration by each of seven mobile DNA elements, using >200 genomic feature variables.

types integration transcriptional
Melusin gene (ITGB1BP2) nucleotide variations study in hypertensive and cardiopathic patients.

PMID 20017903 · PMC2803168 · BMC medical genetics · 2009 · 6 claims · 5 setups

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Only three nucleotide variations in ITGB1BP2 were found among 928 screened subjects, indicating a high degree of conservation of the gene in the populations analyzed

genomic hela itgb1bp2 melusin direct minigene in-silico
A variant of the SLC10A2 gene encoding the apical sodium-dependent bile acid transporter is a risk factor for gallstone disease.

PMID 19823678 · PMC2757911 · PloS one · 2009 · 6 claims · 4 setups

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SLC10A2 is a novel susceptibility gene for cholelithiasis in humans

genomic pooled sanger maldi-tof genotype-phenotype
DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes.

PMID 15608249 · PMC539965 · Nucleic acids research · 2005 · 5 claims · 8 setups

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Comparative human-mouse genome analysis identifies conserved sequence tags (CSTs, >=70% identity over >=100bp) that frequently correspond to non-coding elements with putative regulatory or structural roles

identified cst csts comparative coding exon
GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs.

PMID 17178752 · PMC1781107 · Nucleic acids research · 2007 · 8 claims · 5 setups

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GenomeTrafac is a web-accessible database enabling genome-wide detection of conserved cis-element clusters in human-mouse gene orthologs, covering both conventional and microRNA genes

human-mouse genome blastz-aligned itgb1bp2 comparative transcription sequence
Genetic variants of chemokine receptor CCR7 in patients with systemic lupus erythematosus, Sjogren's syndrome and systemic sclerosis.

PMID 17587445 · PMC1913537 · BMC genetics · 2007 · 6 claims · 4 setups

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CCR7 gene variants occur at extremely low frequency (allelic frequencies ≤5%) in the German population

genomic hut78 t-cells direct pcr dual
A novel variable number of tandem repeat of the natriuretic peptide precursor B gene's 5'-flanking region is associated with essential hypertension among Japanese females.

PMID 17554401 · PMC1885554 · International journal of medical sciences · 2007 · 8 claims · 6 setups

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A novel VNTR polymorphism (TTTC repeat) was discovered at -1241 nucleotides in the 5'-flanking region of NPPB, with 8 alleles ranging from 9 to 19 repeats.

genomic plasma serum n=317 pcr-sscp nucleotide genotyping

Experiments

Comparative genomics and experimental promoter analysis reveal functional liver-specific elements in mammalian hepatic lipase genes.

Assessing the genomic evidence for conserved transcribed pseudogenes under selection.

Genomic profiling of microRNA and messenger RNA reveals deregulated microRNA expression in prostate cancer.

MutScreener: primer design tool for PCR-direct sequencing.

Comparative genomic study reveals a transition from TA richness in invertebrates to GC richness in vertebrates at CpG flanking sites: an indication for context-dependent mutagenicity of methylated CpG sites.

Intronic alternative splicing regulators identified by comparative genomics in nematodes.

Retinitis pigmentosa: mutation analysis of RHO, PRPF31, RP1, and IMPDH1 genes in patients from India.

Adequate use of allele frequencies in Hispanics--a problem elucidated in nephrotic syndrome.

Two previously proposed P1/P2-differentiating and nine novel polymorphisms at the A4GALT (Pk) locus do not correlate with the presence of the P1 blood group antigen.

Genetic analysis of three Korean patients with clinical features of Ehlers-Danlos syndrome type IV.

In silico comparative genomic analysis of GABAA receptor transcriptional regulation.

Glucokinase gene mutations: structural and genotype-phenotype analyses in MODY children from South Italy.

Single-track sequencing for genotyping of multiple SNPs in the N-acetyltransferase 1 (NAT1) gene.

Selection of target sites for mobile DNA integration in the human genome.

Melusin gene (ITGB1BP2) nucleotide variations study in hypertensive and cardiopathic patients.

A variant of the SLC10A2 gene encoding the apical sodium-dependent bile acid transporter is a risk factor for gallstone disease.

DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes.

GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs.

Genetic variants of chemokine receptor CCR7 in patients with systemic lupus erythematosus, Sjogren's syndrome and systemic sclerosis.

A novel variable number of tandem repeat of the natriuretic peptide precursor B gene's 5'-flanking region is associated with essential hypertension among Japanese females.