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 34

System / cell line: microarray ✕ Assay: conserved ✕ Clear

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

Full-text index only

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
Evolutionarily conserved and diverged alternative splicing events show different expression and functional profiles.

PMID 16195578 · PMC1240112 · Nucleic acids research · 2005 · 8 claims · 5 setups

Full-text index only

Alternative splices in 10,818 human-mouse gene pairs can be classified as conserved, novel, or diverged based on genomic and transcript-level cross-species comparison.

orthologous diverse tissues gene comparative est microarray
Integrative functional genomics.

PMID 15239826 · PMC463286 · Genome biology · 2004 · 8 claims · 8 setups

Full-text index only

Ultra-conserved noncoding elements exist across human, mouse and rat genomes at very high sequence identity, often far from genes

yeast tissue-cultured mammalian genomic comparative targeted chip-chip
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
TFBScluster web server for the identification of mammalian composite regulatory elements.

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

Full-text index only

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
miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes.

PMID 16381831 · PMC1347497 · Nucleic acids research · 2006 · 6 claims · 6 setups

Full-text index only

miRNAMap integrates known miRNA genes from miRBase, literature-curated validated targets, and computationally predicted miRNA genes and targets for human, mouse, rat and dog.

conserved putative mirna-target normal comparative machine mirna
Application of genomics to toxicology research.

PMID 12634120 · PMC1241273 · Environmental health perspectives · 2002 · 8 claims · 3 setups

Full-text index only

Toxic chemical exposures alter gene expression, producing a diagnostic transcriptional 'fingerprint' that can be matched against known toxicants to classify untested chemicals' toxic potential.

yeast rodents rodent microarray proposed cross-species
Web-based resources for comparative genomics.

PMID 16197736 · PMC3525128 · Human genomics · 2005 · 8 claims · 8 setups

Full-text index only

Comparative genomics is an indispensable tool for identifying functional genome elements and exploring evolutionary genome dynamics

yeast chimpanzee mammalian protein-coding comparative genome maximum-likelihood
Identifying synonymous regulatory elements in vertebrate genomes.

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

Full-text index only

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
Comparative genomics comes of age.

PMID 12186641 · PMC139393 · Genome biology · 2002 · 8 claims · 8 setups

Full-text index only

Only about 50% of conserved sequence elements (exons+introns) in orthologous human-mouse genes correspond to exons, implying substantial non-exonic conservation

orthologous chromosome chimpanzee somatic-cell comparative targeted tiled
Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach.

PMID 15693947 · PMC551538 · Genome biology · 2005 · 7 claims · 8 setups

Full-text index only

FastCompare, a non-alignment-based, linear-time algorithm, computes a genome-wide conservation score for all k-mers (7-9 nt) between two genomes to identify conserved regulatory elements

cerevisiae elegans randomized computational randomized microarray
CoMoDis: composite motif discovery in mammalian genomes.

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

Full-text index only

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
Population genomics of human gene expression.

PMID 17873874 · PMC2683249 · Nature genetics · 2007 · 8 claims · 8 setups

Full-text index only

Gene expression levels in lymphoblastoid cell lines are a heritable trait

ebv-transformed ceu lymphoblastoid unrelated genome-wide custom cis-eqtl
Zebrafish whole-adult-organism chemogenomics for large-scale predictive and discovery chemical biology.

PMID 18618001 · PMC2442223 · PLoS genetics · 2008 · 8 claims · 6 setups

Full-text index only

Zebrafish whole-adult-organism chemogenomics generates robust prediction models that discriminate P(H)AHs from ECs across independent experiments

zebrafish computational seven consolidated whole-adult-organism supervised quantitative
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
Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates.

PMID 19906729 · PMC2808989 · Nucleic acids research · 2010 · 8 claims · 6 setups

Full-text index only

Patrocles is a database compiling DSPs predicted to perturb miRNA-mediated gene regulation across seven vertebrate species, covering targets, miRNA precursors and silencing machinery.

3'-utr mirbase hapmap comparative snp mirna
Ab initio identification of putative human transcription factor binding sites by comparative genomics.

PMID 15865625 · PMC1097714 · BMC bioinformatics · 2005 · 8 claims · 5 setups

Full-text index only

An integrated algorithm combining human-mouse genomic comparison, motif overrepresentation, and coregulation filters (GO annotation and microarray coexpression) can identify candidate transcription factor binding sites genome-wide

human-mouse conserved gene consensus comparative statistical gene
Splicing bioinformatics to biology.

PMID 16732900 · PMC1779529 · Genome biology · 2006 · 8 claims · 8 setups

Full-text index only

Mutually exclusive selection of Dscam exon 6 variants is governed by base pairing between a conserved intronic docking site and selector sequences adjacent to each alternative exon.

dscam alternative heterologous expressing comparative dicodon reporter
Multiple whole genome alignments and novel biomedical applications at the VISTA portal.

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

Full-text index only

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
Identification of the Wheat (Triticum aestivum) IQD Gene Family and an Expression Analysis of Candidate Genes Associated with Seed Dormancy and Germination.

PMID 35456910 · PMC9025732 · International journal of molecular sciences · 2022 · 8 claims · 8 setups

Has reproduction · 78

73 IQD gene family members (TaIQD1-73) were identified in the wheat genome and phylogenetically divided into six major groups.

triticum taiqd wheat promoter genome-wide phylogenetic synteny

Experiments

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

Evolutionarily conserved and diverged alternative splicing events show different expression and functional profiles.

Integrative functional genomics.

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

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

miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes.

Application of genomics to toxicology research.

Web-based resources for comparative genomics.

Identifying synonymous regulatory elements in vertebrate genomes.

Comparative genomics comes of age.

Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach.

CoMoDis: composite motif discovery in mammalian genomes.

Population genomics of human gene expression.

Zebrafish whole-adult-organism chemogenomics for large-scale predictive and discovery chemical biology.

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

Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates.

Ab initio identification of putative human transcription factor binding sites by comparative genomics.

Splicing bioinformatics to biology.

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

Identification of the Wheat (Triticum aestivum) IQD Gene Family and an Expression Analysis of Candidate Genes Associated with Seed Dormancy and Germination.