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 21

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

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
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
Identifying synonymous regulatory elements in vertebrate genomes.

PMID 15980499 · PMC1160227 · Nucleic acids research · 2005 · 7 claims · 4 setups

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SynoR is a tool that performs de novo genome-wide identification of synonymous regulatory elements (SREs) using evolutionarily conserved TFBS modules as seeds

genome genes genome-wide gene tissue-specificity
DiRE: identifying distant regulatory elements of co-expressed genes.

PMID 18487623 · PMC2447744 · Nucleic acids research · 2008 · 8 claims · 4 setups

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DiRE predicts distant regulatory elements by combining gene co-expression data, comparative genomics and TFBS profiles to determine TFBS-association signatures

liver myod transgenic microarray tfbs enhancer
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
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
Multiple whole genome alignments and novel biomedical applications at the VISTA portal.

PMID 17488840 · PMC1933192 · Nucleic acids research · 2007 · 8 claims · 4 setups

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A novel multiple whole-genome alignment algorithm treats all genomes symmetrically, avoiding dependence on a single base/reference genome

genome vertebrate multi-species whole-genome conservation non-synonymous
Differential Hsp90-dependent gene expression is strain-specific and common among yeast strains.

PMID 37138775 · PMC10149407 · iScience · 2023 · 8 claims · 7 setups

Has reproduction · 100

Hsp90-dependent gene expression varies among different yeast strains

diverse same yeast genomes rna-seq v-src growth
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
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
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
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
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
TFBScluster web server for the identification of mammalian composite regulatory elements.

PMID 16845063 · PMC1538905 · Nucleic acids research · 2006 · 7 claims · 5 setups

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TFBScluster is a web server that identifies genome-wide clusters of TFBSs conserved in multiple mammalian species using human or mouse as the reference genome.

imr90 tissues dog transgenic microarray-based gene
RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12.

PMID 35584008 · PMC9465075 · Microbial genomics · 2022 · 8 claims · 7 setups

Has reproduction · 61

RegulonDB 11.0 is a radical upgrade offering access to more than 2000 high-throughput datasets on transcriptional regulation in E. coli K-12.

coli chip-seq chip-exo gselex
CoMoDis: composite motif discovery in mammalian genomes.

PMID 17130158 · PMC1702496 · Nucleic acids research · 2007 · 7 claims · 4 setups

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CoMoDis is a new bioinformatics tool that streamlines computational identification of novel regulatory modules starting from a single seed motif

ncbi35 gata-1 gene imr90 computational microarray seed-motif-anchored
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
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
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

Experiments

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

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

Identifying synonymous regulatory elements in vertebrate genomes.

DiRE: identifying distant regulatory elements of co-expressed genes.

Inferring combinatorial regulation of transcription in silico.

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

Multiple whole genome alignments and novel biomedical applications at the VISTA portal.

Differential Hsp90-dependent gene expression is strain-specific and common among yeast strains.

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

INTERFEROME: the database of interferon regulated genes.

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

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

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

TFBScluster web server for the identification of mammalian composite regulatory elements.

RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12.

CoMoDis: composite motif discovery in mammalian genomes.

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

In silico comparative genomic analysis of GABAA receptor transcriptional regulation.

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.