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: type ✕ Assay: promoter ✕ Clear

Discovery of genes activated by the mitochondrial unfolded protein response (mtUPR) and cognate promoter elements.

PMID 17849004 · PMC1964532 · PloS one · 2007 · 8 claims · 5 setups

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mtUPR responsive genes (YME1L1, MPPβ, Tim17A, NDUFB2, Endonuclease G, Thioredoxin 2, plus previously known ClpP, Cpn60/10, MtDnaJ) all contain a CHOP element in their promoters

genome cos-7 promoters bioinformatic promoter-luciferase site-directed
Neuroscience in the era of functional genomics and systems biology.

PMID 19829370 · PMC3645852 · Nature · 2009 · 8 claims · 7 setups

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Omics/discovery-based approaches do not eschew hypotheses but elevate hypothesis testing to high-throughput hypothesis generation and prioritization.

developing hippocampus bac-transgenic fetal situ gene bac-transgenic
Differentiation of core promoter architecture between plants and mammals revealed by LDSS analysis.

PMID 17855401 · PMC2094075 · Nucleic acids research · 2007 · 7 claims · 8 setups

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LDSS analysis identifies octamer sequences with localized distribution profiles as promoter constituents, classifiable into groups (REG, TATA, Inr, Kozak, CpG, Y Patch)

arabidopsis rice promoter cross-species ldss sequence distribution
The promoter and the enhancer region of the KLK 3 (prostate specific antigen) gene is frequently mutated in breast tumours and in breast carcinoma cell lines.

PMID 10188912 · PMC2362704 · British journal of cancer · 1999 · 7 claims · 5 setups

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No mutations were found in the protein-coding exons of the PSA gene in breast tumours or cell lines

breast genomic immunofluorometric receptor pcr
Genetic variation in PARL influences mitochondrial content.

PMID 19862556 · PMC2829432 · Human genetics · 2010 · 7 claims · 5 setups

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PARL is a key regulator of mitochondrial integrity and function and plays a role in cellular apoptosis

genomic nuclear parl pcr snp real-time
Lymphocytes from patients with type 1 diabetes display a distinct profile of chromatin histone H3 lysine 9 dimethylation: an epigenetic study in diabetes.

PMID 18776137 · PMC2584123 · Diabetes · 2008 · 6 claims · 7 setups

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Lymphocytes (but not monocytes) from type 1 diabetic patients show a distinct subset of genes with significantly increased H3K9me2 compared with healthy controls.

blood pooled gene chip-chip conventional quantitative
Methylation patterns of the nasal epigenome of hospitalized SARS-CoV-2 positive patients reveal insights into molecular mechanisms of COVID-19.

PMID 40170038 · PMC11963311 · BMC medical genomics · 2025 · 8 claims · 5 setups

Has reproduction

The nasal methylome shows differential DNA methylation in intergenic regions and low methylated regions (LMRs), highlighting distal regulatory/enhancer-like elements in COVID-19 gene regulation

nasal aggregated severe differentially genome methylation differential
Involvement of HTLV-I Tax and CREB in aneuploidy: a bioinformatics approach.

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

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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
Transcriptional regulation of human eosinophil RNases by an evolutionary- conserved sequence motif in primate genome.

PMID 17927842 · PMC2174947 · BMC molecular biology · 2007 · 7 claims · 8 setups

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A 34-nt sequence motif (-81 to -48) is present in all primate edn promoters and in macaque ecp promoter but is deleted in other primate ecp promoters

primate hepg2 32p-labeled sequence rt-pcr luciferase
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
Evolutionary repair: Changes in multiple functional modules allow meiotic cohesin to support mitosis.

PMID 32155147 · PMC7138332 · PLoS biology · 2020 · 8 claims · 8 setups

Has reproduction · 90

Replacing the mitotic kleisin Scc1 with the meiotic kleisin Rec8 impairs sister chromosome cohesion, advances genome replication timing, and reduces reproductive fitness by 45%.

cerevisiae parallel evolved rec8-expressing competitive experimental whole-genome
Construction and analysis of tag single nucleotide polymorphism maps for six human-mouse orthologous candidate genes in type 1 diabetes.

PMID 15720714 · PMC551616 · BMC genetics · 2005 · 7 claims · 5 setups

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None of the six candidate gene regions showed evidence of association with type 1 diabetes (all multi-locus/single-locus test P values > 0.2)

genomic case-control nramp1 type sanger snp microsatellite
Identification of a novel functional deletion variant in the 5'-UTR of the DJ-1 gene.

PMID 19825160 · PMC2767350 · BMC medical genetics · 2009 · 8 claims · 6 setups

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A novel 16 bp deletion variant (g.-6_+10del) was identified in the DJ-1 5'-UTR, spanning the transcription start site, 93 bp downstream of a known Sp1 site.

genomic hek293 m17 south sscp dual-luciferase pcr-rflp
Deep transcriptomics reveals cell-specific isoforms of pan-neuronal genes.

PMID 40379625 · PMC12084633 · Nature communications · 2025 · 8 claims · 5 setups

Has reproduction · 84

Pan-neuronal genes (expressed in many/all neurons) harbor highly cell-specific splice variants/isoforms restricted to single or few neuron types.

elegans short-read whole-animal rt-pcr
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
Transgenerational inheritance of an acquired small RNA-based antiviral response in C. elegans.

PMID 22119442 · PMC3250924 · Cell · 2011 · 8 claims · 8 setups

Has reproduction · 68

viRNA-mediated silencing of the FR1gfp Flock House virus is transmitted to RNAi-deficient (rde-1 or rde-4 homozygous) progeny and persists for many ensuing generations, i.e. an acquired antiviral trait is inherited.

transgenic elegans four gfp genetic template-independence
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

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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
Finding the needle in the haystack: why high-throughput screening is good for your health.

PMID 12100740 · PMC138735 · Breast cancer research : BCR · 2002 · 8 claims · 8 setups

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HTS is essential for finding lead compounds, especially for novel targets whose active-site structure is unknown

raf-1 mitotic mutant tumor biochemical cell-based conformational
The loss of transcriptional inhibition by the photoreceptor-cell specific nuclear receptor (NR2E3) is not a necessary cause of enhanced S-cone syndrome.

PMID 17438525 · PMC2669504 · Molecular vision · 2007 · 8 claims · 8 setups

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NR2E3 LBD fused to a heterologous Gal4 DBD mediates dose-dependent transcriptional repression on Gal4-responsive reporters.

cos-1 hela luciferase western electrophoretic
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

Experiments

Discovery of genes activated by the mitochondrial unfolded protein response (mtUPR) and cognate promoter elements.

Neuroscience in the era of functional genomics and systems biology.

Differentiation of core promoter architecture between plants and mammals revealed by LDSS analysis.

The promoter and the enhancer region of the KLK 3 (prostate specific antigen) gene is frequently mutated in breast tumours and in breast carcinoma cell lines.

Genetic variation in PARL influences mitochondrial content.

Lymphocytes from patients with type 1 diabetes display a distinct profile of chromatin histone H3 lysine 9 dimethylation: an epigenetic study in diabetes.

Methylation patterns of the nasal epigenome of hospitalized SARS-CoV-2 positive patients reveal insights into molecular mechanisms of COVID-19.

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

Transcriptional regulation of human eosinophil RNases by an evolutionary- conserved sequence motif in primate genome.

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

Evolutionary repair: Changes in multiple functional modules allow meiotic cohesin to support mitosis.

Construction and analysis of tag single nucleotide polymorphism maps for six human-mouse orthologous candidate genes in type 1 diabetes.

Identification of a novel functional deletion variant in the 5'-UTR of the DJ-1 gene.

Deep transcriptomics reveals cell-specific isoforms of pan-neuronal genes.

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

Transgenerational inheritance of an acquired small RNA-based antiviral response in C. elegans.

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

Finding the needle in the haystack: why high-throughput screening is good for your health.

The loss of transcriptional inhibition by the photoreceptor-cell specific nuclear receptor (NR2E3) is not a necessary cause of enhanced S-cone syndrome.

INTERFEROME: the database of interferon regulated genes.