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 38

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

Sequence occurrence and structural uniqueness of a G-quadruplex in the human c-kit promoter.

PMID 17720713 · PMC2034477 · Nucleic acids research · 2007 · 8 claims · 4 setups

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The native 22-nt c-kit87 sequence occurs only once in the entire human genome.

genome synthetic c-kit87 c-kit genome-wide circular molecular
Genetic microheterogeneity and phenotypic variation of Helicobacter pylori arginase in clinical isolates.

PMID 17408487 · PMC1853099 · BMC microbiology · 2007 · 8 claims · 8 setups

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Arginase activity varies more than 100-fold among H. pylori clinical isolates and laboratory-adapted strains

minimally-passaged pylori coli arginase urease heterologous
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
Molecular phylogeny of the antiangiogenic and neurotrophic serpin, pigment epithelium derived factor in vertebrates.

PMID 17020603 · PMC1609119 · BMC genomics · 2006 · 8 claims · 8 setups

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A single PEDF gene is present in all examined vertebrate species but is absent from invertebrates (D. melanogaster, C. elegans, C. intestinalis)

vertebrate cdna pedf complete genomic rt-pcr phylogenetic
Developments in CORG: a gene-centric comparative genomics resource.

PMID 17135197 · PMC1751536 · Nucleic acids research · 2007 · 7 claims · 4 setups

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CORG provides pairwise and multiple sequence alignments of upstream promoter regions and whole gene loci across 10 vertebrate species.

upstream gene overlapping c-fos pairwise sequence comparative
Single nucleotide extension technology for quantitative site-specific evaluation of metC/C in GC-rich regions.

PMID 15958788 · PMC1150895 · Nucleic acids research · 2005 · 6 claims · 4 setups

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SNaPshot primers with mismatches to upstream bisulfite-induced C/T or G/A polymorphisms produce a position-dependent biasing effect of up to 70%, decreasing as the mismatch moves farther upstream of the target cytosine

comt synthetic genomic snapshot
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
Cis-Regulation of the CFTR Gene in Pancreatic Cells.

PMID 40332394 · PMC12027686 · International journal of molecular sciences · 2025 · 7 claims · 8 setups

Has reproduction · 50

Multiple active CREs exist upstream and downstream of the CFTR gene in pancreatic (Capan-1) cells, identified via ATAC-seq, CUT&RUN-seq (H3K27ac), 4C-seq, and the ABC model

capan-1 caco-2 hepg2 atac-seq cut&run-seq 4c-seq
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
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
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

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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
U7 snRNAs: a computational survey.

PMID 18267300 · PMC5054213 · Genomics, proteomics & bioinformatics · 2007 · 8 claims · 6 setups

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A computational (BLAST-based) survey identified bona fide U7 snRNA genes with characteristic upstream promoter elements (PSE) across most vertebrate genomes examined, plus numerous pseudogenes.

mammalian drosophilid aligned basal blast sequence consensus
The MAPPER database: a multi-genome catalog of putative transcription factor binding sites.

PMID 15608292 · PMC540057 · Nucleic acids research · 2005 · 8 claims · 6 setups

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Built a library of 1134 HMM models (359 matrix-derived, 718 factor-derived, 57 JASPAR-derived), corresponding to 863 distinct TF names, from TRANSFAC and JASPAR binding site data

genome drosophila transfac b99 profile sequence case-study
g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments.

PMID 17478515 · PMC1933153 · Nucleic acids research · 2007 · 8 claims · 5 setups

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g:Profiler integrates four modules (g:Profiler core, g:Convert, g:Orth, g:Sorter) into a single cross-linked web tool for gene list analysis

input 1000-bp microarray organisms functional transcription gene
Highly individual methylation patterns of alternative glucocorticoid receptor promoters suggest individualized epigenetic regulatory mechanisms.

PMID 19004867 · PMC2602793 · Nucleic acids research · 2008 · 7 claims · 4 setups

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Methylation patterns of the five GR promoters activated in PBMCs are highly variable between individuals.

chromosome genomic pbmc multi-species phylogenetic bisulphite
Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data.

PMID 15921519 · PMC1166541 · BMC bioinformatics · 2005 · 6 claims · 4 setups

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A minimum evolution algorithm (implemented in software 'phyrex') can reconstruct ancestral states of continuous characters like gene expression or splicing levels along a phylogeny

gene upstream chimpanzee reconstructed minimum sequence ancestral
Automatic annotation of eukaryotic genes, pseudogenes and promoters.

PMID 16925832 · PMC1810547 · Genome biology · 2006 · 8 claims · 6 setups

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Fgenesh++ gene prediction pipeline identifies 91% of coding nucleotides with 90% specificity

encode regions genes chromosome computational pseudogene promoter
ABS: a database of Annotated regulatory Binding Sites from orthologous promoters.

PMID 16381947 · PMC1347478 · Nucleic acids research · 2006 · 7 claims · 6 setups

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ABS is a public database of experimentally identified TF binding sites conserved in orthologous vertebrate gene promoters, manually curated from the literature.

orthologous literature sequence pairwise
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
INTERFEROME: the database of interferon regulated genes.

PMID 18996892 · PMC2686605 · Nucleic acids research · 2009 · 8 claims · 6 setups

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INTERFEROME is an open-access database integrating IRG expression data with annotation, orthologue sequences from 37 species, tissue expression, and gene regulatory (TFBS) information

chimp ifn-treated tissues irg microarray in-house basal

Experiments

Sequence occurrence and structural uniqueness of a G-quadruplex in the human c-kit promoter.

Genetic microheterogeneity and phenotypic variation of Helicobacter pylori arginase in clinical isolates.

In silico comparative genomic analysis of GABAA receptor transcriptional regulation.

Molecular phylogeny of the antiangiogenic and neurotrophic serpin, pigment epithelium derived factor in vertebrates.

Developments in CORG: a gene-centric comparative genomics resource.

Single nucleotide extension technology for quantitative site-specific evaluation of metC/C in GC-rich regions.

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

Cis-Regulation of the CFTR Gene in Pancreatic Cells.

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

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

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

U7 snRNAs: a computational survey.

The MAPPER database: a multi-genome catalog of putative transcription factor binding sites.

g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments.

Highly individual methylation patterns of alternative glucocorticoid receptor promoters suggest individualized epigenetic regulatory mechanisms.

Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data.

Automatic annotation of eukaryotic genes, pseudogenes and promoters.

ABS: a database of Annotated regulatory Binding Sites from orthologous promoters.

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

INTERFEROME: the database of interferon regulated genes.