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 158

System / cell line: gene ✕ Assay: factor ✕ 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

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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
Onto-Tools: new additions and improvements in 2006.

PMID 17584796 · PMC1933142 · Nucleic acids research · 2007 · 8 claims · 3 setups

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OE2GO enables functional profiling for organisms lacking public-domain annotations by allowing users to supply custom GO-format annotation files and OBO-format ontology files

specified pathway functional example
Recent additions and improvements to the Onto-Tools.

PMID 15980579 · PMC1160233 · Nucleic acids research · 2005 · 7 claims · 3 setups

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The Onto-Tools back-end database was redesigned around the Entrez Gene data model after NCBI phased out LocusLink in February 2005.

homo example mus functional pathway cross-database
Genomic view of the evolution of the complement system.

PMID 16896831 · PMC2480602 · Immunogenetics · 2006 · 8 claims · 6 setups

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Bony fish and higher vertebrates share practically the same set of complement genes, indicating most complement gene duplications occurred by the teleost/mammalian divergence (~500 MYA)

chicken complement sponge shark comparative phylogenetic reverse
Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data.

PMID 15921519 · PMC1166541 · BMC bioinformatics · 2005 · 6 claims · 4 setups

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A minimum evolution algorithm (implemented in software 'phyrex') can reconstruct ancestral states of continuous characters like gene expression or splicing levels along a phylogeny

gene upstream chimpanzee reconstructed minimum sequence ancestral
The lords of the genomes.

PMID 15461811 · PMC545592 · Genome biology · 2004 · 8 claims · 8 setups

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Functionally active clusters of transcription-factor binding sites are evolutionarily conserved between Drosophila species, whereas inactive clusters are not, even when sequence identity alone cannot distinguish them

drosophila cdna-derived saccharomyces acid reporter-gene enhancer chromatin
Gata-3 and mammary cell fate.

PMID 17381824 · PMC1868924 · Breast cancer research : BCR · 2007 · 8 claims · 8 setups

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Gata-3 is required for formation of mammary placodes during embryonic development

mammary gata-3 k14-cre mmtv-cre microarray lacz cre
Molecular phylogeny of the antiangiogenic and neurotrophic serpin, pigment epithelium derived factor in vertebrates.

PMID 17020603 · PMC1609119 · BMC genomics · 2006 · 8 claims · 8 setups

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A single PEDF gene is present in all examined vertebrate species but is absent from invertebrates (D. melanogaster, C. elegans, C. intestinalis)

vertebrate cdna pedf complete genomic rt-pcr phylogenetic
Exploration of the omics evidence landscape: adding qualitative labels to predicted protein-protein interactions.

PMID 17880677 · PMC2375035 · Genome biology · 2007 · 7 claims · 8 setups

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Combining pairs of omics evidence types into two-dimensional 'evidence landscapes' allows regions to be identified that specifically and purely predict either physical or metabolic protein interactions

saccharomyces correlated chip-chip gene
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
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
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
Alexander Meissner: learning the reprogramming code.

PMID 19704017 · PMC2733751 · The Journal of cell biology · 2009 · 8 claims · 6 setups

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A defined set of factors present in oocytes and embryonic stem (ES) cells can reprogram a somatic cell to pluripotency, as shown by nuclear transfer and ES cell/somatic cell fusion experiments

blastocysts somatic fused genomic nuclear inducible fusion
Proneural-mesenchymal antagonism dominates the patterns of phenotypic heterogeneity in glioblastoma.

PMID 38433919 · PMC10905000 · iScience · 2024 · 8 claims · 8 setups

Has reproduction · 100

The four proposed GBM molecular subtypes (Proneural, Neural, Classical, Mesenchymal / NPC-like, OPC-like, AC-like, MES-like) are not mutually exclusive or independent of one another

scrna-seq tcga-gbm gse131928 tumor gene pairwise principal
T Cells With Activated STAT4 Drive the High-Risk Rejection State to Renal Allograft Failure After Kidney Transplantation.

PMID 35844542 · PMC9283858 · Frontiers in immunology · 2022 · 8 claims · 8 setups

Has reproduction · 78

Unsupervised UMAP/Leiden clustering of 2,611 microarray datasets reveals 6 rejection states that diverge from traditional Banff clinical classification

kidney scrna-seq microarray meblack microarray single-cell scissor
Gene module regulation in dilated cardiomyopathy and the role of Na/K-ATPase.

PMID 35901050 · PMC9333241 · PloS one · 2022 · 5 claims · 8 setups

Has reproduction · 55

Several co-expressed gene modules are significantly associated with left ventricle ejection fraction (LVEF) and the DCM phenotype, enriched in fibrosis-related, small molecule transporting-related, and immune response-related pathways.

heart degs gene rna-seq bulk differential gene
GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets.

PMID 40208796 · PMC11984350 · GigaScience · 2025 · 8 claims · 8 setups

Has reproduction · 76

GeneSetCart is a web-based platform that lets users assemble, augment, combine, visualize, and analyze gene sets from multiple sources in one place

user-assembled archs4 generif-derived aggregated gene gene-gene literature
Identification of intrinsic genes across general hypertension, hypertension with left ventricular remodeling, and uncontrolled hypertension.

PMID 36277786 · PMC9582241 · Frontiers in cardiovascular medicine · 2022 · 7 claims · 8 setups

Has reproduction · 73

FBXW4 and 13 other genes are uniquely enriched in the general hypertension group

peripheral white four gse75360 microarray gene weighted
The distribution of SNPs in human gene regulatory regions.

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

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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
GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs.

PMID 17178752 · PMC1781107 · Nucleic acids research · 2007 · 8 claims · 5 setups

Full-text index only

GenomeTrafac is a web-accessible database enabling genome-wide detection of conserved cis-element clusters in human-mouse gene orthologs, covering both conventional and microRNA genes

human-mouse genome blastz-aligned itgb1bp2 comparative transcription sequence

Experiments

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

Onto-Tools: new additions and improvements in 2006.

Recent additions and improvements to the Onto-Tools.

Genomic view of the evolution of the complement system.

Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data.

The lords of the genomes.

Gata-3 and mammary cell fate.

Molecular phylogeny of the antiangiogenic and neurotrophic serpin, pigment epithelium derived factor in vertebrates.

Exploration of the omics evidence landscape: adding qualitative labels to predicted protein-protein interactions.

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

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

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

Alexander Meissner: learning the reprogramming code.

Proneural-mesenchymal antagonism dominates the patterns of phenotypic heterogeneity in glioblastoma.

T Cells With Activated STAT4 Drive the High-Risk Rejection State to Renal Allograft Failure After Kidney Transplantation.

Gene module regulation in dilated cardiomyopathy and the role of Na/K-ATPase.

GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets.

Identification of intrinsic genes across general hypertension, hypertension with left ventricular remodeling, and uncontrolled hypertension.

The distribution of SNPs in human gene regulatory regions.

GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs.