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 111

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

G-quadruplexes in promoters throughout the human genome.

PMID 17169996 · PMC1802602 · Nucleic acids research · 2007 · 8 claims · 6 setups

Full-text index only

Promoter regions (1 kb upstream of TSS) are significantly enriched in quadruplex motifs (PQS) relative to the rest of the genome

genome quiescent gene synthetic computational nuclease gene
Evolutionary comparison provides evidence for pathogenicity of RMRP mutations.

PMID 16244706 · PMC1262189 · PLoS genetics · 2005 · 7 claims · 5 setups

Full-text index only

Putative pathogenic RMRP mutations are located in highly conserved nucleotides across mammals, whereas polymorphisms are located in non-conserved positions.

genomic rmrp family non-finnish sequencing comparative microsatellite
CLC-2 single nucleotide polymorphisms (SNPs) as potential modifiers of cystic fibrosis disease severity.

PMID 15507145 · PMC526769 · BMC medical genetics · 2004 · 8 claims · 7 setups

Full-text index only

PCR amplification and sequencing of CLC-2 revealed 1 SNP in the promoter, 4 SNPs in intron 1, and none in exon 20

nasal genomic ib3-1 western pcr fisher's
Heterotachy in mammalian promoter evolution.

PMID 16683025 · PMC1449885 · PLoS genetics · 2006 · 8 claims · 5 setups

Full-text index only

The rate of promoter evolution relative to control sequences is not consistent between or within mammalian lineages over time (heterotachy)

promoter ancient chimpanzee comparative ancient micro-indel
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

Full-text index only

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

5'-flanking upstream transiently genomic comparative tfbs promoter-reporter
A pharmacogenetics study of the human glucuronosyltransferase UGT1A4.

PMID 19890225 · PMC6177227 · Pharmacogenetics and genomics · 2009 · 7 claims · 6 setups

Full-text index only

Extensive sequencing of UGT1A4 (promoter to exon 1+2000bp) identified numerous novel polymorphisms: 13 intronic, 39 promoter, and 14 exonic variants (10 causing amino acid changes)

genomic hek293 hepg2 microsomes pcr site-directed luciferase
Sequence changes in predicted promoter elements of STK11/LKB1 are unlikely to contribute to Peutz-Jeghers syndrome.

PMID 15774015 · PMC1084245 · BMC genomics · 2005 · 6 claims · 4 setups

Full-text index only

Integrated phylogenetic foot printing and transcription factor binding site (TFBS) prediction identified a consensus putative STK11/LKB1 promoter region between nucleotides -1090 and -1472

genomic phylogenetic direct high
Mutation screening and haplotype analysis of the rhodopsin gene locus in Japanese patients with retinitis pigmentosa.

PMID 17653048 · PMC2776539 · Molecular vision · 2007 · 8 claims · 4 setups

Full-text index only

No RP patient among 68 Japanese subjects carried a RHO mutation causing an amino acid substitution

blood-derived genomic chromosomes rho whole-locus pcr haplotype
Tissue plasminogen activator and plasminogen activator inhibitor type 1 gene polymorphism in patients with gastric ulcer complicated with bleeding.

PMID 12589088 · PMC3054991 · Journal of Korean medical science · 2003 · 6 claims · 5 setups

Full-text index only

The t-PA I/D or D/D genotype is significantly associated with duodenal (vs gastric) ulcer location

genomic randomly patients endoscopic allele-specific pcr logistic
GREM, a technique for genome-wide isolation and quantitative analysis of promoter active repeats.

PMID 16698959 · PMC3303178 · Nucleic acids research · 2006 · 7 claims · 5 setups

Full-text index only

GREM enables genome-wide isolation and quantitative analysis of transcriptionally active (promoter-active) repetitive elements while excluding read-through transcript background

testicular genomic coli grem rt-pcr race
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

Full-text index only

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
Identification of polymorphisms and balancing selection in the male infertility candidate gene, ornithine decarboxylase antizyme 3.

PMID 16542438 · PMC1526716 · BMC medical genetics · 2006 · 8 claims · 6 setups

Full-text index only

Mutations in the OAZ3 gene are not a common cause of male infertility

genomic coding inferred oaz3 direct sscp haplotype
Deletion of dinucleotide repeat (Delta 14 allele) in the methylthioadenosine phosphorylase (MTAP) promoter and the allelotype of MTAP promoter in the Japanese population.

PMID 11985785 · PMC5927014 · Japanese journal of cancer research : Gann · 2002 · 8 claims · 4 setups

Full-text index only

DHL-9 lymphoma cells lack detectable MTAP enzyme activity despite possessing an intact (non-deleted) MTAP gene

dhl-9 genomic lymphoblastoid hela pcr allele-specific luciferase
Method for determination of (-102C>T) single nucleotide polymorphism in the human manganese superoxide dismutase promoter.

PMID 15598343 · PMC544190 · BMC genetics · 2004 · 6 claims · 4 setups

Full-text index only

A novel TaqMan allelic discrimination assay can reliably genotype the MnSOD -102C>T SNP from diverse DNA sources including blood, buccal swabs, frozen tissue, and paraffin blocks.

genomic paraffin-embedded taqman pcr-restriction automated
Genetic variation in PARL influences mitochondrial content.

PMID 19862556 · PMC2829432 · Human genetics · 2010 · 7 claims · 5 setups

Full-text index only

PARL is a key regulator of mitochondrial integrity and function and plays a role in cellular apoptosis

genomic nuclear parl pcr snp real-time
Inactivation of O6-methylguanine-DNA methyltransferase by promoter CpG island hypermethylation in gastric cancers.

PMID 12085181 · PMC2375420 · British journal of cancer · 2002 · 6 claims · 8 setups

Full-text index only

Loss of MGMT expression in gastric carcinomas frequently results from promoter CpG island hypermethylation.

gastric consecutive snu-620 methylation-specific immunohistochemistry western
Array-based analysis of genomic DNA methylation patterns of the tumour suppressor gene p16INK4A promoter in colon carcinoma cell lines.

PMID 15860770 · PMC1087791 · Nucleic acids research · 2005 · 8 claims · 4 setups

Full-text index only

A Geniom One-synthesized oligonucleotide microarray can determine the methylation status of individual CpG dinucleotides in parallel, combining high throughput with single-base resolution

hct116 p16 genomic methylation-specific combined oligonucleotide
Expression of RAB4B, a protein governing endocytic recycling, is co-regulated with MHC class II genes.

PMID 17175541 · PMC1802633 · Nucleic acids research · 2007 · 7 claims · 7 setups

Full-text index only

A typical MHC-II-like S-Y module is present upstream of the RAB4B transcription start site, identified by genome-wide profile scanning

genomic raji monocyte-derived rj2.2.5 computational chip-on-chip chromatin
Single nucleotide polymorphisms in bone turnover-related genes in Koreans: ethnic differences in linkage disequilibrium and haplotype.

PMID 18036257 · PMC2222243 · BMC medical genetics · 2007 · 8 claims · 5 setups

Full-text index only

Resequencing 81 candidate osteoporosis genes in 24 Koreans identified 942 variants (888 SNPs, 43 indels, 11 microsatellites)

genomic sequenced korean common sanger sequence population
Resequencing PNMT in European hypertensive and normotensive individuals: no common susceptibilily variants for hypertension and purifying selection on intron 1.

PMID 17645789 · PMC1947951 · BMC medical genetics · 2007 · 7 claims · 7 setups

Full-text index only

Resequencing of PNMT found no common susceptibility variants that distinguish hypertensive from normotensive individuals

genomic pnmt promoter pcr population haplotype

Experiments

G-quadruplexes in promoters throughout the human genome.

Evolutionary comparison provides evidence for pathogenicity of RMRP mutations.

CLC-2 single nucleotide polymorphisms (SNPs) as potential modifiers of cystic fibrosis disease severity.

Heterotachy in mammalian promoter evolution.

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

A pharmacogenetics study of the human glucuronosyltransferase UGT1A4.

Sequence changes in predicted promoter elements of STK11/LKB1 are unlikely to contribute to Peutz-Jeghers syndrome.

Mutation screening and haplotype analysis of the rhodopsin gene locus in Japanese patients with retinitis pigmentosa.

Tissue plasminogen activator and plasminogen activator inhibitor type 1 gene polymorphism in patients with gastric ulcer complicated with bleeding.

GREM, a technique for genome-wide isolation and quantitative analysis of promoter active repeats.

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

Identification of polymorphisms and balancing selection in the male infertility candidate gene, ornithine decarboxylase antizyme 3.

Deletion of dinucleotide repeat (Delta 14 allele) in the methylthioadenosine phosphorylase (MTAP) promoter and the allelotype of MTAP promoter in the Japanese population.

Method for determination of (-102C>T) single nucleotide polymorphism in the human manganese superoxide dismutase promoter.

Genetic variation in PARL influences mitochondrial content.

Inactivation of O6-methylguanine-DNA methyltransferase by promoter CpG island hypermethylation in gastric cancers.

Array-based analysis of genomic DNA methylation patterns of the tumour suppressor gene p16INK4A promoter in colon carcinoma cell lines.

Expression of RAB4B, a protein governing endocytic recycling, is co-regulated with MHC class II genes.

Single nucleotide polymorphisms in bone turnover-related genes in Koreans: ethnic differences in linkage disequilibrium and haplotype.

Resequencing PNMT in European hypertensive and normotensive individuals: no common susceptibilily variants for hypertension and purifying selection on intron 1.