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 129

System / cell line: promoter ✕ Assay: sequence ✕ Clear

Linking disease-associated genes to regulatory networks via promoter organization.

PMID 15701758 · PMC549397 · Nucleic acids research · 2005 · 8 claims · 7 setups

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Pairs of TFBSs conserved both vertically (orthologous genes) and horizontally (co-regulated genes) can serve as seeds to build promoter models representing potential co-regulation networks

orthologous eukaryotic genomatix pubmed promoter model additional
Sequence changes in predicted promoter elements of STK11/LKB1 are unlikely to contribute to Peutz-Jeghers syndrome.

PMID 15774015 · PMC1084245 · BMC genomics · 2005 · 6 claims · 4 setups

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Integrated phylogenetic foot printing and transcription factor binding site (TFBS) prediction identified a consensus putative STK11/LKB1 promoter region between nucleotides -1090 and -1472

genomic phylogenetic direct high
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
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
EPD in its twentieth year: towards complete promoter coverage of selected model organisms.

PMID 16381980 · PMC1347508 · Nucleic acids research · 2006 · 7 claims · 4 setups

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EPD is an annotated, non-redundant collection of experimentally defined eukaryotic POL II promoters accessed via genome position pointers.

rice preliminary primer sequence quality
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
Pol II promoter prediction using characteristic 4-mer motifs: a machine learning approach.

PMID 18834544 · PMC2575220 · BMC bioinformatics · 2008 · 8 claims · 8 setups

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128 discriminating 4-mer motifs combined with an SVM (RBF kernel, LIBSVM) can distinguish promoter from non-promoter DNA sequences

plant drosophila promoter same 4-mer tata blast
Deletion of dinucleotide repeat (Delta 14 allele) in the methylthioadenosine phosphorylase (MTAP) promoter and the allelotype of MTAP promoter in the Japanese population.

PMID 11985785 · PMC5927014 · Japanese journal of cancer research : Gann · 2002 · 8 claims · 4 setups

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DHL-9 lymphoma cells lack detectable MTAP enzyme activity despite possessing an intact (non-deleted) MTAP gene

dhl-9 genomic lymphoblastoid hela pcr allele-specific luciferase
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
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
Methylation of class II transactivator gene promoter IV is not associated with susceptibility to multiple sclerosis.

PMID 18606010 · PMC2464579 · BMC medical genetics · 2008 · 6 claims · 4 setups

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Methylation of the MHC2TA promoter pIV is not associated with MS susceptibility; no methylation was detected in any twin sample regardless of disease status

peripheral mhc2ta pcr sanger bisulfite cpg
Interaction of vitamin D receptor with HLA DRB1 0301 in type 1 diabetes patients from North India.

PMID 19956544 · PMC2780726 · PloS one · 2009 · 8 claims · 6 setups

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Interaction between VDR and HLA alleles is mediated by a VDRE present in the promoter region of HLA-DRB1*0301, which may be detrimental in the absence of 1,25-(OH)2D3 in early childhood.

blood genotype hla-drb1*0301 drb1*0301-carrying pcr-rflp pcr haplotype
Malaria severity and human nitric oxide synthase type 2 (NOS2) promoter haplotypes.

PMID 19859740 · PMC2939908 · Human genetics · 2010 · 7 claims · 7 setups

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NOS2 promoter haplotypes are not consistently associated with malaria severity or malarial anemia across three independent Tanzanian study populations

tanzanian a549 muheza-tanga sscp pcr restriction
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
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
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
Transcription of the human and rodent SPAM1 / PH-20 genes initiates within an ancient endogenous retrovirus.

PMID 15804358 · PMC1079825 · BMC genomics · 2005 · 8 claims · 8 setups

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Human, mouse, and rat SPAM1/Spam1 transcripts initiate within an ERV1 pol (internal coding) region rather than within an LTR

testis panel genome 5'-race non-quantitative
Viruses take center stage in cellular evolution.

PMID 16787527 · PMC1779534 · Genome biology · 2006 · 8 claims · 6 setups

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A large poxvirus-like dsDNA virus may have become the eukaryotic nucleus after being taken in by an ancestral cell (viral eukaryogenesis)

acanthamoeba coccolithovirus nucleocytoplasmic dsdna whole-genome phylogenetic comparative
Peroxisomal proliferator activated receptor-gamma deficiency in a Canadian kindred with familial partial lipodystrophy type 3 (FPLD3).

PMID 16412238 · PMC1368963 · BMC medical genetics · 2006 · 8 claims · 6 setups

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A novel PPARG nonsense mutation, Y355X, was identified in a mother and daughter with FPLD3-consistent phenotypes and was absent from unaffected relatives and 260 healthy controls

subjects nih3t3 subject healthy sequencing luciferase western
Implication of BRCA2 -26G>A 5' untranslated region polymorphism in susceptibility to sporadic breast cancer and its modulation by p53 codon 72 Arg>Pro polymorphism.

PMID 17945002 · PMC2242669 · Breast cancer research : BCR · 2007 · 8 claims · 7 setups

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-26G>A polymorphism in the BRCA2 5' UTR is functional: the A allele drives roughly twice the reporter gene expression of the G allele in MCF-7 and HeLa cells

mcf-7 hela brca2 peripheral luciferase transcription genotyping

Experiments

Linking disease-associated genes to regulatory networks via promoter organization.

Sequence changes in predicted promoter elements of STK11/LKB1 are unlikely to contribute to Peutz-Jeghers syndrome.

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

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

EPD in its twentieth year: towards complete promoter coverage of selected model organisms.

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

Pol II promoter prediction using characteristic 4-mer motifs: a machine learning approach.

Deletion of dinucleotide repeat (Delta 14 allele) in the methylthioadenosine phosphorylase (MTAP) promoter and the allelotype of MTAP promoter in the Japanese population.

The distribution of SNPs in human gene regulatory regions.

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

Methylation of class II transactivator gene promoter IV is not associated with susceptibility to multiple sclerosis.

Interaction of vitamin D receptor with HLA DRB1 0301 in type 1 diabetes patients from North India.

Malaria severity and human nitric oxide synthase type 2 (NOS2) promoter haplotypes.

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

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

The genome of the ant Tetramorium bicarinatum reveals a tandem organization of venom peptides genes allowing the prediction of their regulatory and evolutionary profiles.

Transcription of the human and rodent SPAM1 / PH-20 genes initiates within an ancient endogenous retrovirus.

Viruses take center stage in cellular evolution.

Peroxisomal proliferator activated receptor-gamma deficiency in a Canadian kindred with familial partial lipodystrophy type 3 (FPLD3).

Implication of BRCA2 -26G>A 5' untranslated region polymorphism in susceptibility to sporadic breast cancer and its modulation by p53 codon 72 Arg>Pro polymorphism.