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 68

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

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

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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
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

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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
CpG island methylation status and mutation analysis of the RB1 gene essential promoter region and protein-binding pocket domain in nervous system tumours.

PMID 12556968 · PMC2376780 · British journal of cancer · 2003 · 8 claims · 4 setups

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RB1 CpG island hypermethylation is a common epigenetic event associated with development of malignant nervous system tumours

nervous bisulphite-modified same pcr-sscp methylation-specific bisulphite
A novel polymorphism in the 1A promoter region of the vitamin D receptor is associated with altered susceptibilty and prognosis in malignant melanoma.

PMID 15238985 · PMC2364794 · British journal of cancer · 2004 · 7 claims · 6 setups

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A novel A-1012G (adenine-guanine) polymorphism exists in the VDR exon 1a promoter region, identified by SSCP screening and sequencing

blood variant patients same sscp sanger pcr-rflp
CHD5, a tumor suppressor gene deleted from 1p36.31 in neuroblastomas.

PMID 18577749 · PMC2483574 · Journal of the National Cancer Institute · 2008 · 7 claims · 8 setups

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CHD5 promoter is highly methylated in neuroblastoma cell lines with 1p deletion and absent CHD5 expression (NLF, IMR5)

neuroblastoma nlf athymic methylation-specific quantitative soft
Characterization of the human DYRK1A promoter and its regulation by the transcription factor E2F1.

PMID 18366763 · PMC2292204 · BMC molecular biology · 2008 · 8 claims · 8 setups

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Transcription start sites of human DYRK1A are distributed over an 800 bp region within an unmethylated CpG island

pc3 saos2 resting phoenix 5'-race-pcr rt-pcr chip-seq
Adverse prognosis of epigenetic inactivation in RUNX3 gene at 1p36 in human pancreatic cancer.

PMID 18475302 · PMC2391125 · British journal of cancer · 2008 · 7 claims · 5 setups

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RUNX3 promoter hypermethylation is frequent in primary pancreatic cancer tissue

pancreatic microsatellite methylation-specific bisulphite
The pharmacogenomics of membrane transporters project: research at the interface of genomics and transporter pharmacology.

PMID 19940846 · PMC2923224 · Clinical pharmacology and therapeutics · 2010 · 8 claims · 8 setups

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PMT identified sequence variants in 129 membrane transporter genes in the SLC and ABC superfamilies, discovering over 3100 SNPs

sophie mammalian xenopus lymphoblastoid resequencing cellular heterologous
Mutation analysis of the MSMB gene in familial prostate cancer.

PMID 19997100 · PMC2816656 · British journal of cancer · 2010 · 8 claims · 5 setups

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No deleterious mutations were found in the MSMB coding region in 192 familial prostate cancer cases

germline blood 161-nt genotype sanger taqman transcription
Large-scale structural analysis of the core promoter in mammalian and plant genomes.

PMID 16049029 · PMC1181242 · Nucleic acids research · 2005 · 8 claims · 7 setups

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DNA encodes at least two independent levels of functional information: protein/TF-binding sequence information and physical/structural properties of the molecule itself.

core-promoter arabidopsis rice computational adaptive linear
Interaction of vitamin D receptor with HLA DRB1 0301 in type 1 diabetes patients from North India.

PMID 19956544 · PMC2780726 · PloS one · 2009 · 8 claims · 6 setups

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Interaction between VDR and HLA alleles is mediated by a VDRE present in the promoter region of HLA-DRB1*0301, which may be detrimental in the absence of 1,25-(OH)2D3 in early childhood.

blood genotype hla-drb1*0301 drb1*0301-carrying pcr-rflp pcr haplotype
Mutation screen and association studies in the diacylglycerol O-acyltransferase homolog 2 gene (DGAT2), a positional candidate gene for early onset obesity on chromosome 11q13.

PMID 17477860 · PMC1871603 · BMC genetics · 2007 · 7 claims · 5 setups

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DGAT2 is a plausible positional and functional candidate gene for obesity due to its localization at chr.11q13 (a linkage region) and its key role in triglyceride synthesis

extremely families genome sanger case-control family-based
Hypomethylation and expression of BEX2, IGSF4 and TIMP3 indicative of MLL translocations in acute myeloid leukemia.

PMID 19835597 · PMC2770485 · Molecular cancer · 2009 · 8 claims · 8 setups

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MLL-mutant (MLL mu) AML cell lines show significantly lower TSG promoter methylation than MLL wild-type (MLL wt) AML cell lines

acute mll lines bone ms-mlpa hhai methylation-specific
Evolutionary comparison provides evidence for pathogenicity of RMRP mutations.

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

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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
Epigenetics and phenotypic variation in mammals.

PMID 16688527 · PMC3906716 · Mammalian genome : official journal of the International Mammalian Genome Society · 2006 · 8 claims · 8 setups

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Epigenetic modifications are mitotically heritable, but the fidelity of meiotic/transgenerational inheritance in mammals is poorly understood and evidence in mammals is scanty.

mammalian mhc chromosomes embryonic methylation high-throughput chip
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
Array-based profiling of reference-independent methylation status (aPRIMES) identifies frequent promoter methylation and consecutive downregulation of ZIC2 in pediatric medulloblastoma.

PMID 17344319 · PMC1874664 · Nucleic acids research · 2007 · 7 claims · 7 setups

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aPRIMES is a novel array-based method that detects direct (absolute) methylation status of CGIs via competitive hybridization of McrBC-digested (methylated) versus HpaII/BstUI-digested (unmethylated) DNA from the same genome, avoiding reference-tissue and copy-number biases

pediatric tumor eight desmoplastic aprimes bisulfite quantitative
Genes implicated in multiple sclerosis pathogenesis from consilience of genotyping and expression profiles in relapse and remission.

PMID 18366677 · PMC2324081 · BMC medical genetics · 2008 · 8 claims · 7 setups

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Distinct sets of dysregulated genes are found in peripheral blood during the relapse phase versus the remission phase of RRMS

peripheral blood pooled trio gene quantitative promoter
Microsatellite instability and mismatch repair gene inactivation in sporadic pancreatic and colon tumours.

PMID 10389971 · PMC2363009 · British journal of cancer · 1999 · 6 claims · 5 setups

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Microsatellite instability is common in sporadic pancreatic cancer but occurs at a uniformly low rate and is not accompanied by hMLH1/hMSH2 alterations, suggesting it does not drive pancreatic tumorigenesis.

sporadic msi-positive tumour unstable microsatellite denaturing sequencing
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

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

genomic pnmt promoter pcr population haplotype

Experiments

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

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

CpG island methylation status and mutation analysis of the RB1 gene essential promoter region and protein-binding pocket domain in nervous system tumours.

A novel polymorphism in the 1A promoter region of the vitamin D receptor is associated with altered susceptibilty and prognosis in malignant melanoma.

CHD5, a tumor suppressor gene deleted from 1p36.31 in neuroblastomas.

Characterization of the human DYRK1A promoter and its regulation by the transcription factor E2F1.

Adverse prognosis of epigenetic inactivation in RUNX3 gene at 1p36 in human pancreatic cancer.

The pharmacogenomics of membrane transporters project: research at the interface of genomics and transporter pharmacology.

Mutation analysis of the MSMB gene in familial prostate cancer.

Large-scale structural analysis of the core promoter in mammalian and plant genomes.

Interaction of vitamin D receptor with HLA DRB1 0301 in type 1 diabetes patients from North India.

Mutation screen and association studies in the diacylglycerol O-acyltransferase homolog 2 gene (DGAT2), a positional candidate gene for early onset obesity on chromosome 11q13.

Hypomethylation and expression of BEX2, IGSF4 and TIMP3 indicative of MLL translocations in acute myeloid leukemia.

Evolutionary comparison provides evidence for pathogenicity of RMRP mutations.

Epigenetics and phenotypic variation in mammals.

In silico comparative genomic analysis of GABAA receptor transcriptional regulation.

Array-based profiling of reference-independent methylation status (aPRIMES) identifies frequent promoter methylation and consecutive downregulation of ZIC2 in pediatric medulloblastoma.

Genes implicated in multiple sclerosis pathogenesis from consilience of genotyping and expression profiles in relapse and remission.

Microsatellite instability and mismatch repair gene inactivation in sporadic pancreatic and colon tumours.

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