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 40

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

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

Full-text index only

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
Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment.

PMID 16925837 · PMC1810552 · Genome biology · 2006 · 6 claims · 3 setups

Full-text index only

Promoter predictors that combine promoter prediction with gene prediction (N-SCAN, Fprom) achieve better performance than pure ab initio promoter predictors, mainly by reducing the promoter search space and false positives

genome encode computational tss manual
TRED: a transcriptional regulatory element database, new entries and other development.

PMID 17202159 · PMC1899102 · Nucleic acids research · 2007 · 8 claims · 3 setups

Full-text index only

TRED collects mammalian cis- and trans-regulatory elements together with experimental evidence, mapped onto assembled genomes

cancer-related computational literature database
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

Full-text index only

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
Genomics of signaling crosstalk of estrogen receptor alpha in breast cancer cells.

PMID 18365014 · PMC2268000 · PloS one · 2008 · 7 claims · 6 setups

Full-text index only

Estrogen, growth factors and cAMP elicit surprisingly distinct ERα-dependent transcriptional responses in MCF7 cells

mcf7 promoter cdna quantitative computational
Involvement of HTLV-I Tax and CREB in aneuploidy: a bioinformatics approach.

PMID 16822311 · PMC1553470 · Retrovirology · 2006 · 8 claims · 6 setups

Full-text index only

CTLL cells stably expressing wild-type Tax (CTLL/WT) show higher aneuploidy than a CREB-transactivation-deficient Tax clone (CTLL/703)

ctll gene promoter metaphase microarray bioinformatics
Large-scale discovery and validation of functional elements in the human genome.

PMID 15774039 · PMC1088940 · Genome biology · 2005 · 8 claims · 8 setups

Full-text index only

Genome-wide tiling microarray hybridization reveals large, diverse sets of transcripts, many of which lack existing gene annotations

liver genome yeast lines tiling computational dnase
SNP@Promoter: a database of human SNPs (single nucleotide polymorphisms) within the putative promoter regions.

PMID 18315851 · PMC2259403 · BMC bioinformatics · 2008 · 8 claims · 4 setups

Full-text index only

SNP@Promoter is a database of human SNPs within putative promoter regions and predicted transcription factor binding sites

genome predicted target computational snp evolutionary
Large-scale structural analysis of the core promoter in mammalian and plant genomes.

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

Full-text index only

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
G-quadruplexes in promoters throughout the human genome.

PMID 17169996 · PMC1802602 · Nucleic acids research · 2007 · 8 claims · 6 setups

Full-text index only

Promoter regions (1 kb upstream of TSS) are significantly enriched in quadruplex motifs (PQS) relative to the rest of the genome

genome quiescent gene synthetic computational nuclease gene
Prediction-based approaches to characterize bidirectional promoters in the mammalian genome.

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

Full-text index only

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
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

Full-text index only

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
Automatic annotation of eukaryotic genes, pseudogenes and promoters.

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

Full-text index only

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

encode regions genes chromosome computational pseudogene promoter
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

Full-text index only

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
The distribution of SNPs in human gene regulatory regions.

PMID 16209714 · PMC1260019 · BMC genomics · 2005 · 8 claims · 6 setups

Full-text index only

SNPs occur with higher density closer to the transcriptional start site within gene promoter regions than in further upstream regions

gene mammalian promoter experimentally genome-wide computational binding
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

Full-text index only

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
G-quadruplexes: the beginning and end of UTRs.

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

Full-text index only

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
Institutional Profile: The University of California Pharmacogenomics Center: at the interface of genomics, biological mechanisms and drug therapy.

PMID 19842929 · PMC2923222 · Pharmacogenomics · 2009 · 8 claims · 8 setups

Full-text index only

Approximately 15-20% of nonsynonymous variants in membrane transporters exhibit reduced function

abc hek293 expressing sophie computational transporter transport
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

Full-text index only

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
Application of alternative de novo motif recognition models for analysis of structural heterogeneity of transcription factor binding sites: a case study of FOXA2 binding sites.

PMID 34547062 · PMC8408018 · Vavilovskii zhurnal genetiki i selektsii · 2021 · 6 claims · 7 setups

Has reproduction · 62

Combining four de novo models (PWM, diPWM, BaMM, InMoDe) significantly increases the fraction of recognized peaks versus PWM alone (by 26.3%).

hg38 foxa2 pwm whole-genome chip-seq pwm dipwm

Experiments

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

Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment.

TRED: a transcriptional regulatory element database, new entries and other development.

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

Genomics of signaling crosstalk of estrogen receptor alpha in breast cancer cells.

Involvement of HTLV-I Tax and CREB in aneuploidy: a bioinformatics approach.

Large-scale discovery and validation of functional elements in the human genome.

SNP@Promoter: a database of human SNPs (single nucleotide polymorphisms) within the putative promoter regions.

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

G-quadruplexes in promoters throughout the human genome.

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

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

Automatic annotation of eukaryotic genes, pseudogenes and promoters.

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

The distribution of SNPs in human gene regulatory regions.

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

G-quadruplexes: the beginning and end of UTRs.

Institutional Profile: The University of California Pharmacogenomics Center: at the interface of genomics, biological mechanisms and drug therapy.

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

Application of alternative de novo motif recognition models for analysis of structural heterogeneity of transcription factor binding sites: a case study of FOXA2 binding sites.