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 19

System / cell line: regions ✕ Assay: tfbs ✕ Clear

Inferring combinatorial regulation of transcription in silico.

PMID 15647509 · PMC546154 · Nucleic acids research · 2005 · 8 claims · 5 setups

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Combining Cluster-Buster (TFBS cluster prediction) with GOSSIP (rigorous GO enrichment statistics with multiple-testing/FDR correction) predicts biological functions controlled by combinatorial transcription factor action, without prior knowledge of factor targets

upstream monocytes same tfbs microarray permutation
oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets.

PMID 22973536 · PMC3429929 · G3 (Bethesda, Md.) · 2012 · 8 claims · 6 setups

Has reproduction · 49

oPOSSUM-3 is a web-accessible system that identifies over-represented TFBS and TFBS families in DNA sequences of co-expressed genes or in sequences from high-throughput methods such as ChIP-Seq.

hg19 large-scale gene-based jaspar tfbs sequence-based anchored
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
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
BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.

PMID 16845052 · PMC1538844 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Babelomics is presented as an updated, complete suite of web tools for functional analysis of genome-scale experiments with new and improved modules

pre-selected pre-tabulated genes ranked kegg expression text-mining
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
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
High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites.

PMID 18988630 · PMC2662491 · Nucleic acids research · 2009 · 8 claims · 8 setups

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Incorporating H3K4me3 chromatin modification estimates greatly improves the accuracy of in silico prediction of in vivo TF binding for a wide range of TFs in human and mouse

embryonic neural t-cells mm8 chip-seq chip-chip pwm
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
Identification of direct regulatory targets of the transcription factor Sox10 based on function and conservation.

PMID 18786246 · PMC2556353 · BMC genomics · 2008 · 6 claims · 6 setups

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PLP, Sox10, SOD3, and Ptn are direct regulatory targets of Sox10, confirmed by chromatin immunoprecipitation binding to conserved cis-elements

rt4d6 gst-sox10 microarray comparative real
Allelic imbalance in gene expression as a guide to cis-acting regulatory single nucleotide polymorphisms in cancer cells.

PMID 17267408 · PMC1865061 · Nucleic acids research · 2007 · 6 claims · 6 setups

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Measuring allelic imbalance (AI) of two SNP alleles within the same sample is an effective approach for identifying cis-acting rSNPs, since each allele serves as an internal control for the other.

tumor promoter hela cdna bead tag-microarray
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
Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing.

PMID 19822575 · PMC2794179 · Nucleic acids research · 2009 · 8 claims · 6 setups

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ChIP-seq identified 3064 GABP peaks, 7266 FOXA2 peaks and 18783 HNF4a peaks in HepG2 cells

hepg2 liver chip-seq quantitative co-immunoprecipitation
miRGen 2.0: a database of microRNA genomic information and regulation.

PMID 19850714 · PMC2808909 · Nucleic acids research · 2010 · 7 claims · 6 setups

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miRGen 2.0 is a database providing comprehensive information about the genomic position of human and mouse microRNA coding transcripts and their regulation by transcription factors

lung organ malme embryonic polii small nucleosome
The genome of the ant Tetramorium bicarinatum reveals a tandem organization of venom peptides genes allowing the prediction of their regulatory and evolutionary profiles.

PMID 38245722 · PMC10800049 · BMC genomics · 2024 · 8 claims · 8 setups

Has reproduction · 100

44 venom peptide genes were identified, distributed across four of the eleven chromosomes and organized in tandem repeat clusters.

tetramorium bicarinatum vpg venom whole-genome blast gene
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
Motif discovery in promoters of genes co-localized and co-expressed during myeloid cells differentiation.

PMID 19059999 · PMC2632922 · Nucleic acids research · 2009 · 6 claims · 8 setups

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A novel multi-step computational method (built on approximate pattern enumeration, binomial over-representation scoring with FDR correction, and k-medoids clustering) can identify over-represented motifs in a selected set of promoters relative to a background promoter set.

myeloid reference selected genome-localized microarray promoter k-medoids
Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons.

PMID 19969543 · PMC2831330 · Nucleic acids research · 2010 · 8 claims · 8 setups

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38 candidate cis-regulatory coding exons (RCEs) with predicted target genes were identified genome-wide

hg18 zebrafish bystander human-mouse comparative synteny orthologous
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

Inferring combinatorial regulation of transcription in silico.

oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets.

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

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

BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.

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

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

High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites.

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

Identification of direct regulatory targets of the transcription factor Sox10 based on function and conservation.

Allelic imbalance in gene expression as a guide to cis-acting regulatory single nucleotide polymorphisms in cancer cells.

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

Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing.

miRGen 2.0: a database of microRNA genomic information and regulation.

The genome of the ant Tetramorium bicarinatum reveals a tandem organization of venom peptides genes allowing the prediction of their regulatory and evolutionary profiles.

In silico comparative genomic analysis of GABAA receptor transcriptional regulation.

Motif discovery in promoters of genes co-localized and co-expressed during myeloid cells differentiation.

Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons.

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