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 78

System / cell line: target ✕ Assay: gene-expression ✕ Clear

Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data.

PMID 35473573 · PMC9044877 · Genome biology · 2022 · 8 claims · 8 setups

Has reproduction

Combining multiple enhancer-definition and enhancer-gene link data sources yields 1860 genome-wide EnTDefs covering >500 cell types

types encode chip-seq chromhmm dnase-seq
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

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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

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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
CRSD: a comprehensive web server for composite regulatory signature discovery.

PMID 16845073 · PMC1538777 · Nucleic acids research · 2006 · 7 claims · 5 setups

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CRSD is a comprehensive web server integrating six large-scale databases (UniGene, mature microRNAs, putative promoter, TRANSFAC, pathway, GO) plus two newly constructed genome-wide databases (MRS and TRS) for composite regulatory signature discovery

gene 3'-utr promoter user-submitted genome-wide microrna binding
Genome-wide location analysis and expression studies reveal a role for p110 CUX1 in the activation of DNA replication genes.

PMID 18003658 · PMC2248751 · Nucleic acids research · 2008 · 8 claims · 8 setups

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p110 CUX1 is recruited to promoters of cell cycle-related target genes preferentially during S phase

hela hs578t nih3t3 genomic chap-chip conventional scanning
Thermodynamic stability and Watson-Crick base pairing in the seed duplex are major determinants of the efficiency of the siRNA-based off-target effect.

PMID 18988625 · PMC2602766 · Nucleic acids research · 2008 · 8 claims · 6 setups

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Thermodynamic stability (Tm and standard free-energy change, ΔG) of the seed duplex is a major determinant of siRNA off-target effect efficiency

hela protein-free dual-luciferase reporter thermodynamic
Promoting human promoters.

PMID 16760901 · PMC1681504 · Molecular systems biology · 2006 · 8 claims · 5 setups

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A computational protocol using MARS on known sequence motifs can quantify transcription factor effects on human gene expression despite noise and data size challenges

gene liver cycle genes computational expression time-course
Single-cell transcriptomics and chromatin accessibility profiling elucidate the kidney-protective mechanism of mineralocorticoid receptor antagonists.

PMID 37906287 · PMC10760974 · The Journal of clinical investigation · 2024 · 8 claims · 7 setups

Has reproduction · 95

Mineralocorticoid (DOCA) effects are established through open chromatin and target gene expression primarily in principal and connecting tubule cells, and to a lesser extent in distal convoluted tubule (DCT2) cells.

kidney doca-salt serum heart single-nucleus bulk physiology
Adaptively inferring human transcriptional subnetworks.

PMID 16760900 · PMC1681499 · Molecular systems biology · 2006 · 8 claims · 7 setups

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A multivariate linear spline (MARS-based) model correlating PWM binding scores with log expression ratios can identify active cis-motif combinations in mammalian promoters without requiring gene clustering.

liver proximal hela predicted microarray computational novo
Genome-wide analysis of MEF2 transcriptional program reveals synaptic target genes and neuronal activity-dependent polyadenylation site selection.

PMID 19109909 · PMC2630178 · Neuron · 2008 · 8 claims · 8 setups

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MEF2 directly regulates a genome-wide program of 182 activity-dependent target genes in hippocampal neurons

e18 hippocampal forebrain profiling rt-qpcr chip-chip
Novel insights into adipogenesis from omics data.

PMID 19689276 · PMC2765082 · Current medicinal chemistry · 2009 · 8 claims · 8 setups

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Pparg and Cebpa are the two master transcriptional regulators governing adipogenesis

3t3-l1 embryonic multipotent nih-3t3 microarray gel non-gel-based
Innate immune modulation by RNA viruses: emerging insights from functional genomics.

PMID 18654572 · PMC7097543 · Nature reviews. Immunology · 2008 · 8 claims · 7 setups

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Influenza virus signals primarily through RIG-I to induce ISG expression, while West Nile virus signals through both RIG-I and MDA5 cooperatively.

embryonic liver brain serial gene-expression computational
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
Expression genomics in breast cancer research: microarrays at the crossroads of biology and medicine.

PMID 17397520 · PMC1868923 · Breast cancer research : BCR · 2007 · 8 claims · 8 setups

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Genome-wide expression microarray studies reveal transcriptional networks/signatures that explain breast cancer biological and clinical heterogeneity

breast early-stage diffuse dlbcl gene
Defining human diabetic nephropathy on the molecular level: integration of transcriptomic profiles with biological knowledge.

PMID 18704688 · PMC2597685 · Reviews in endocrine & metabolic disorders · 2008 · 8 claims · 8 setups

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Genetic predisposition determines susceptibility and rate of progression to ESRD in diabetic patients, in addition to environmental factors

kidney proximal pbmcs macrophages gene qrt-pcr immunohistochemistry
Constructing an APOBEC-related gene signature with predictive value in the overall survival and therapeutic sensitivity in lung adenocarcinoma.

PMID 37954334 · PMC10637964 · Heliyon · 2023 · 8 claims · 8 setups

Has reproduction · 88

APOBEC family genes are aberrantly expressed across cancers, with APOBEC3B the most consistently upregulated, and APOBEC3B/APOBEC3A are markedly altered in LUAD

tcga tcga-luad geo beas-2b bulk somatic microarray
In vivo application of RNA interference: from functional genomics to therapeutics.

PMID 16096010 · PMC7112075 · Advances in genetics · 2005 · 7 claims · 7 setups

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RNAi operates through two mechanistically related but distinct pathways: cytoplasmic delivery of siRNA duplexes and nuclear delivery of shRNA expression cassettes that mimic miRNA

mice tumor laser-induced herpetic cationic intraperitoneal aqueous
Single-Cell Transcriptome Analysis Revealed Heterogeneity and Identified Novel Therapeutic Targets for Breast Cancer Subtypes.

PMID 37190091 · PMC10137100 · Cells · 2023 · 8 claims · 8 setups

Has reproduction · 54

Single-cell transcriptomic analysis of EPCAM+Lin- epithelial cells identified unique gene signatures/markers that distinguish ER+, HER2+, ER+HER2+, and TNBC molecular subtypes

breast epcam+cd45-cd8a-cd4-cd19-cd3e cancer identified single-cell differential crispr-cas9
miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes.

PMID 18029362 · PMC2238982 · Nucleic acids research · 2008 · 8 claims · 6 setups

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miRNAMap 2.0 is a resource collecting experimentally verified miRNAs and experimentally verified miRNA target genes in human, mouse, rat and other metazoan genomes

major tissues conserved predicted quantitative bead-based microarray
Deciphering the Immune Microenvironment at the Forefront of Tumor Aggressiveness by Constructing a Regulatory Network with Single-Cell and Spatial Transcriptomic Data.

PMID 38254989 · PMC10815467 · Genes · 2024 · 8 claims · 8 setups

Has reproduction · 85

Combining scRNA-seq and spatial transcriptomics enables inference of malignant cells at the invasive front of the ER+ breast cancer TME and dissection of events at the tumor infiltration forefront

normal er+ epithelial malignant single-cell spatial copy

Experiments

Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data.

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

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

CRSD: a comprehensive web server for composite regulatory signature discovery.

Genome-wide location analysis and expression studies reveal a role for p110 CUX1 in the activation of DNA replication genes.

Thermodynamic stability and Watson-Crick base pairing in the seed duplex are major determinants of the efficiency of the siRNA-based off-target effect.

Promoting human promoters.

Single-cell transcriptomics and chromatin accessibility profiling elucidate the kidney-protective mechanism of mineralocorticoid receptor antagonists.

Adaptively inferring human transcriptional subnetworks.

Genome-wide analysis of MEF2 transcriptional program reveals synaptic target genes and neuronal activity-dependent polyadenylation site selection.

Novel insights into adipogenesis from omics data.

Innate immune modulation by RNA viruses: emerging insights from functional genomics.

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

Expression genomics in breast cancer research: microarrays at the crossroads of biology and medicine.

Defining human diabetic nephropathy on the molecular level: integration of transcriptomic profiles with biological knowledge.

Constructing an APOBEC-related gene signature with predictive value in the overall survival and therapeutic sensitivity in lung adenocarcinoma.

In vivo application of RNA interference: from functional genomics to therapeutics.

Single-Cell Transcriptome Analysis Revealed Heterogeneity and Identified Novel Therapeutic Targets for Breast Cancer Subtypes.

miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes.

Deciphering the Immune Microenvironment at the Forefront of Tumor Aggressiveness by Constructing a Regulatory Network with Single-Cell and Spatial Transcriptomic Data.