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 30

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

Target SNP selection in complex disease association studies.

PMID 15248903 · PMC487897 · BMC bioinformatics · 2004 · 7 claims · 3 setups

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A computational pipeline can retrieve gene sequence, collect SNP variation data, and annotate SNPs falling in functional motifs (promoter, exon-intron structure, AU-rich elements, TF binding sites, splice sites) with expression in target tissue

genes pooled primer computational maldi-tof blast
Correlating novel variable and conserved motifs in the Hemagglutinin protein with significant biological functions.

PMID 18681973 · PMC2553082 · Virology journal · 2008 · 8 claims · 6 setups

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14 MEME blocks were identified in the HA protein of H3N2 strains (1968-1999), with blocks 1, 2, 3, and 7 correlating with several biological functions

h3n2 meme sequence entropy
CompMoby: comparative MobyDick for detection of cis-regulatory motifs.

PMID 18950538 · PMC2605473 · BMC bioinformatics · 2008 · 7 claims · 4 setups

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CompMoby identifies cis-regulatory binding sites at both transcriptional and post-transcriptional levels in metazoans without prior knowledge of the trans-acting factor

embryonic hela novo genome-wide
G-quadruplexes: the beginning and end of UTRs.

PMID 18832370 · PMC2577360 · Nucleic acids research · 2008 · 8 claims · 5 setups

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UTRs show significant strand asymmetry with C-PQS more common than G-PQS, consistent with general depletion of G-quadruplex-forming RNA

genome 5'-utr simulated protein-coding computational high-resolution utr
Detection of YMDD motif mutants by oligonucleotide chips in lamivudine-untreated patients with chronic hepatitis B virus infection.

PMID 15308845 · PMC2816888 · Journal of Korean medical science · 2004 · 6 claims · 5 setups

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An oligonucleotide chip was developed using probes for wild-type YMDD, M552V, and three M552I probe variants to detect HBV polymerase YMDD motif mutations

serum hbv nested pcr oligonucleotide pcr restriction
Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication.

PMID 16899447 · PMC1557810 · Nucleic acids research · 2006 · 8 claims · 8 setups

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The RE1 PSSM identifies functional RE1 binding sites with greater sensitivity and selectivity than the previously used RE1 consensus sequence

fibroblast hela hek293 set genome-wide electrophoretic rt-pcr
Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data.

PMID 18684996 · PMC2532738 · Nucleic acids research · 2008 · 8 claims · 7 setups

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SISSRs identifies binding sites from ChIP-Seq short reads with much higher resolution than the standard region-clustering approach

cd4+ jurkat hela computational chip-seq novo motif
Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.

PMID 20003482 · PMC2807441 · BMC genomics · 2009 · 8 claims · 6 setups

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Manual annotation of the mouse Chromosome 8 defensin region identifies 98 gene loci: 54 in the alpha-defensin cluster and 44 in the beta-defensin cluster

c57bl orthologous alpha-defensin defensin manual comparative sequence
QuadBase: genome-wide database of G4 DNA--occurrence and conservation in human, chimpanzee, mouse and rat promoters and 146 microbes.

PMID 17962308 · PMC2238983 · Nucleic acids research · 2008 · 8 claims · 3 setups

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QuadBase is a compendium of G4 DNA (quadruplex) motifs focused on their occurrence and conservation in promoters, composed of EuQuad and ProQuad

chimpanzee prokaryotic promoters genome-wide cross-species
A missense mutation in the nuclear localization signal sequence of CERKL (p.R106S) causes autosomal recessive retinal degeneration.

PMID 18978954 · PMC2576480 · Molecular vision · 2008 · 8 claims · 6 setups

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A C>A transversion in exon 2 of CERKL (c.316C>A) causes a missense change p.R106S in the nuclear localization signal sequence (KLKRR) of the protein.

patients genomic family cerkl ophthalmic homozygosity multipoint
Mutation analysis of the MDM4 gene in German breast cancer patients.

PMID 18279506 · PMC2259322 · BMC cancer · 2008 · 8 claims · 8 setups

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Resequencing of the whole MDM4 coding region in 40 German familial breast cancer patients uncovered two coding variants (V74V and D153G) in 4/40 patients

german bilateral mdm4 lymphoid direct rflp-based splice
Multiple distinct sets of stereotyped antigen receptors indicate a role for antigen in promoting chronic lymphocytic leukemia.

PMID 15314077 · PMC2211936 · The Journal of experimental medicine · 2004 · 7 claims · 5 setups

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Five distinct sets of B-CLL patients express strikingly similar (stereotyped) BCRs sharing common H and L chain V region gene segments and similar CDR3 length, composition, and junctional residues.

b-cll sequence cd5+ igv blast phylogenetic
A distinct epigenetic signature at targets of a leukemia protein.

PMID 17266773 · PMC1796549 · BMC genomics · 2007 · 7 claims · 7 setups

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Combining gene expression microarray analysis with bioinformatic search for AML1-consensus sequences identifies direct AML1 targets that expression analysis alone cannot resolve

32d sequence gene bioinformatic real-time
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.

PMID 17478504 · PMC1933151 · Nucleic acids research · 2007 · 8 claims · 8 setups

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FatiGO+ is a web-based tool for functional profiling of genome-scale experiments that integrates functional annotation, regulatory motifs and interaction data

user-supplied gene predicted interactome gene kegg transcription
E3RC: A step-by-step computational protocol for exploring enhancer RNA expression and regulation using conventional RNA-seq data.

PMID 40716058 · PMC12318280 · STAR protocols · 2025 · 6 claims · 3 setups

Has reproduction · 62

E3RC is a computational framework for identifying and quantifying eRNAs and characterizing their expression and transcriptional regulation using conventional RNA-seq data.

preimplantation genome erna bulk computational motif
Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data.

PMID 35473573 · PMC9044877 · Genome biology · 2022 · 8 claims · 8 setups

Has reproduction

Combining multiple enhancer-definition and enhancer-gene link data sources yields 1860 genome-wide EnTDefs covering >500 cell types

types encode chip-seq chromhmm dnase-seq
CEAS: cis-regulatory element annotation system.

PMID 16845068 · PMC1538818 · Nucleic acids research · 2006 · 7 claims · 5 setups

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CEAS is the first web server to streamline genome-scale ChIP-chip downstream analyses for biologists without strong bioinformatics support

genome genomic chip-chip repeat-masked conservation
CTCFBSDB: a CTCF-binding site database for characterization of vertebrate genomic insulators.

PMID 17981843 · PMC2238977 · Nucleic acids research · 2008 · 7 claims · 8 setups

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CTCF is the only identified trans-acting factor in vertebrates that confers enhancer-blocking insulator activity

ohlsson ren zhao tissues chip-chip massive motif
Functional analysis of novel SNPs and mutations in human and mouse genomes.

PMID 19091009 · PMC2638150 · BMC bioinformatics · 2008 · 8 claims · 7 setups

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FANS streamlines functional analysis of novel SNPs and mutations into a simplified, few-click, four-step procedure.

apoe 11-nucleotide sequence genomic manual automated exonic
Concurrent genotyping of Helicobacter pylori virulence genes and human cytokine SNP sites using whole genome amplified DNA derived from minute amounts of gastric biopsy specimen DNA.

PMID 18842150 · PMC2577186 · BMC microbiology · 2008 · 7 claims · 8 setups

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MDA-amplified DNA from minute gastric biopsy specimens enables concurrent PCR-based genotyping of bacterial (H. pylori) and human host genes from a single DNA source

mda-amplified pylori-positive multiplex pyrosequencing pcr

Experiments

Target SNP selection in complex disease association studies.

Correlating novel variable and conserved motifs in the Hemagglutinin protein with significant biological functions.

CompMoby: comparative MobyDick for detection of cis-regulatory motifs.

G-quadruplexes: the beginning and end of UTRs.

Detection of YMDD motif mutants by oligonucleotide chips in lamivudine-untreated patients with chronic hepatitis B virus infection.

Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication.

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data.

Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.

QuadBase: genome-wide database of G4 DNA--occurrence and conservation in human, chimpanzee, mouse and rat promoters and 146 microbes.

A missense mutation in the nuclear localization signal sequence of CERKL (p.R106S) causes autosomal recessive retinal degeneration.

Mutation analysis of the MDM4 gene in German breast cancer patients.

Multiple distinct sets of stereotyped antigen receptors indicate a role for antigen in promoting chronic lymphocytic leukemia.

A distinct epigenetic signature at targets of a leukemia protein.

FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.

E3RC: A step-by-step computational protocol for exploring enhancer RNA expression and regulation using conventional RNA-seq data.

Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data.

CEAS: cis-regulatory element annotation system.

CTCFBSDB: a CTCF-binding site database for characterization of vertebrate genomic insulators.

Functional analysis of novel SNPs and mutations in human and mouse genomes.

Concurrent genotyping of Helicobacter pylori virulence genes and human cytokine SNP sites using whole genome amplified DNA derived from minute amounts of gastric biopsy specimen DNA.