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 91

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

Linking disease-associated genes to regulatory networks via promoter organization.

PMID 15701758 · PMC549397 · Nucleic acids research · 2005 · 8 claims · 7 setups

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Pairs of TFBSs conserved both vertically (orthologous genes) and horizontally (co-regulated genes) can serve as seeds to build promoter models representing potential co-regulation networks

orthologous eukaryotic genomatix pubmed promoter model additional
CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis.

PMID 16381948 · PMC1347397 · Nucleic acids research · 2006 · 6 claims · 2 setups

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CAGE Basic and Analysis Databases together form a comprehensive resource for promoter analysis using CAGE tag data from human and mouse

tested cage race
Prediction-based approaches to characterize bidirectional promoters in the mammalian genome.

PMID 18366609 · PMC2386062 · BMC genomics · 2008 · 8 claims · 7 setups

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The mapping algorithm identified 5,647 candidate bidirectional promoter regions in the mouse genome, similar in number to those previously found in human.

genome seven genes computational cage comparative
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
L1Base: from functional annotation to prediction of active LINE-1 elements.

PMID 15608246 · PMC539998 · Nucleic acids research · 2005 · 7 claims · 6 setups

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L1Base is a database of putatively active LINE-1 insertions in human, mouse and rat genomes, containing FLI-L1s (intact in both ORFs), ORF2-L1s (intact ORF2, disrupted ORF1), and FLnI-L1s (full-length, >6000 bp, non-intact)

sapiens orf1 orf fli-l1s genomic repeatmasker hmm-profile
TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies.

PMID 15608156 · PMC539958 · Nucleic acids research · 2005 · 8 claims · 5 setups

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TRED is a database collecting both cis-regulatory elements (promoters) and trans-regulatory elements (transcription factor binding/regulation data) with linked access.

promoter tred-retrieved computational literature relational
Pol II promoter prediction using characteristic 4-mer motifs: a machine learning approach.

PMID 18834544 · PMC2575220 · BMC bioinformatics · 2008 · 8 claims · 8 setups

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128 discriminating 4-mer motifs combined with an SVM (RBF kernel, LIBSVM) can distinguish promoter from non-promoter DNA sequences

plant drosophila promoter same 4-mer tata blast
The interleukin 12 p40 gene promoter is primed by interferon gamma in monocytic cells.

PMID 8551218 · PMC2192398 · The Journal of experimental medicine · 1996 · 8 claims · 8 setups

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IFN-gamma primes phagocytic cells for LPS-induced transcription of the IL-12 p40 gene rather than directly inducing it

pbmc cell-depleted raw264.7 nuclei ria immunoprecipitation rnase
The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site.

PMID 18367472 · PMC2377430 · Nucleic acids research · 2008 · 8 claims · 5 setups

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1226 eight-letter DNA words show statistically significant positional preferences relative to the TSS across 7914 human promoter regions

putative nonredundant homo genes computational pssm semantic
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

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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
TP73 allelic expression in human brain and allele frequencies in Alzheimer's disease.

PMID 15175114 · PMC420466 · BMC medical genetics · 2004 · 8 claims · 6 setups

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A -386G/A SNP in the TP73 P3 promoter is weakly but significantly associated with AD risk in a tri-ethnic elderly population.

brain peripheral sk-nsh-n genomic rt-pcr direct snp
Inference of transcriptional regulation using gene expression data from the bovine and human genomes.

PMID 17683551 · PMC1978505 · BMC genomics · 2007 · 7 claims · 8 setups

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Using human reference promoter sequences is a useful approach for studying gene expression regulation in species with limited or non-existing genomic sequence, such as cattle.

muscle-specific bovine refseq cardiac novo est blastn
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
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
A pharmacogenetics study of the human glucuronosyltransferase UGT1A4.

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

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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
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
Methylation patterns of the nasal epigenome of hospitalized SARS-CoV-2 positive patients reveal insights into molecular mechanisms of COVID-19.

PMID 40170038 · PMC11963311 · BMC medical genomics · 2025 · 7 claims · 7 setups

Has reproduction

Differential DNA methylation occurs predominantly in intergenic regions and low methylated regions (LMRs), highlighting the role of distal regulatory elements in COVID-19 severity.

nasal aggregated genes differentially whole-genome methylation tiling
In silico promoters: modelling of cis-regulatory context facilitates target predictio.

PMID 18505473 · PMC3823354 · Journal of cellular and molecular medicine · 2009 · 8 claims · 8 setups

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An integrated 'profiling of transcriptional targets' (PTT) strategy by Freebern et al. identified IGF-1 as a co-modulator of immune cell function genes in mitogen/drug-activated T cells.

serca2 rantes genes podocyte-associated literature-based promoter cross-referenced
Malaria severity and human nitric oxide synthase type 2 (NOS2) promoter haplotypes.

PMID 19859740 · PMC2939908 · Human genetics · 2010 · 7 claims · 7 setups

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NOS2 promoter haplotypes are not consistently associated with malaria severity or malarial anemia across three independent Tanzanian study populations

tanzanian a549 muheza-tanga sscp pcr restriction
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

Experiments

Linking disease-associated genes to regulatory networks via promoter organization.

CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis.

Prediction-based approaches to characterize bidirectional promoters in the mammalian genome.

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

L1Base: from functional annotation to prediction of active LINE-1 elements.

TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies.

Pol II promoter prediction using characteristic 4-mer motifs: a machine learning approach.

The interleukin 12 p40 gene promoter is primed by interferon gamma in monocytic cells.

The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site.

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

TP73 allelic expression in human brain and allele frequencies in Alzheimer's disease.

Inference of transcriptional regulation using gene expression data from the bovine and human genomes.

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

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

A pharmacogenetics study of the human glucuronosyltransferase UGT1A4.

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

Methylation patterns of the nasal epigenome of hospitalized SARS-CoV-2 positive patients reveal insights into molecular mechanisms of COVID-19.

In silico promoters: modelling of cis-regulatory context facilitates target predictio.

Malaria severity and human nitric oxide synthase type 2 (NOS2) promoter haplotypes.

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