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 69

System / cell line: 3'-utr ✕ Clear

ARED Organism: expansion of ARED reveals AU-rich element cluster variations between human and mouse.

PMID 17984078 · PMC2238997 · Nucleic acids research · 2008 · 6 claims · 4 setups

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ARED Organism and ARED-Integrated are new/updated public databases cataloguing ARE-containing mRNAs/genes in human, mouse and rat

6x6 ortholog 3'utr comparative chi-squared
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
Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing.

PMID 15885146 · PMC1142312 · BMC genomics · 2005 · 8 claims · 7 setups

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Pig sequence is closer to human than mouse is, across exons, UTRs, introns, intergenic regions, ultra-conserved elements, and miRNAs

sus pig concatenated three-species whole-genome repeat comparative
3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer.

PMID 19917133 · PMC2781828 · BMC genomics · 2009 · 8 claims · 4 setups

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3' tag DGE transcript profiles are highly reproducible between technical and biological replicates, across libraries made at different labs, and across two generations of Illumina Genome Analyzers (GA I and GA II).

brain hbrr topo-cloned tag microarray quantitative
The association of Alu repeats with the generation of potential AU-rich elements (ARE) at 3' untranslated regions.

PMID 15610565 · PMC544599 · BMC genomics · 2004 · 6 claims · 4 setups

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Alu repeats are a source of AREs at 3' UTRs of human mRNA, via poly-A regions of Alu generating complementary poly-T/poly-U regions that acquire regular adenine insertions to form ARE motifs.

utr computationally are repeat positional
ARED 3.0: the large and diverse AU-rich transcriptome.

PMID 16381826 · PMC1347415 · Nucleic acids research · 2006 · 7 claims · 6 setups

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ARED 3.0 computationally mapped more than 4000 ARE-mRNAs to the human genome, representing 5-8% of human genes.

records est est-derived combined computational est sequence
Distribution and effects of nonsense polymorphisms in human genes.

PMID 18852891 · PMC2561068 · PloS one · 2008 · 8 claims · 8 setups

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Nonsense SNPs occur at a lower density than nonsynonymous SNPs, indicating stronger purifying selection against premature stop codons than amino acid changes.

genome genes nonsense snps genome-wide snp codon
Screening for microsatellite instability identifies frequent 3'-untranslated region mutation of the RB1-inducible coiled-coil 1 gene in colon tumors.

PMID 19888451 · PMC2766054 · PloS one · 2009 · 7 claims · 4 setups

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Somatic mutation frequency (%MSI) of 3'UTR microsatellites in MSI-H colorectal tumors correlates significantly with microsatellite length (r=0.86, p=7.2×10−13), following an exponential growth model.

msi-h computational rb1cc1 normal pcr nonlinear real-time
The exonuclease Xrn1 activates transcription and translation of mRNAs encoding membrane proteins.

PMID 30899024 · PMC6428865 · Nature communications · 2019 · 7 claims · 8 setups

Has reproduction · 85

Xrn1 promotes translation of a specific group of mRNAs encoding membrane/secretome proteins, acting at translation initiation.

cerevisiae yeast xrn1∆ western luciferase polysome
Roar: detecting alternative polyadenylation with standard mRNA sequencing libraries.

PMID 27756200 · PMC5069797 · BMC bioinformatics · 2016 · 8 claims · 5 setups

Has reproduction · 75

Roar, a method using PRE/POST read counts around annotated APA sites to compute an m/M ratio and a ratio-of-ratios (roar) statistic, detects differential 3'UTR shortening/lengthening from standard RNA-seq libraries.

testes normal gene rna-seq sapas cdna
Effects of two common polymorphisms in the 3' untranslated regions of estrogen receptor beta on mRNA stability and translatability.

PMID 19754929 · PMC2759954 · BMC genetics · 2009 · 8 claims · 4 setups

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Breast tumor heterozygotes show a significant difference in relative mRNA levels between the two alleles of rs4986938

breast hek293 erβ1 allelic luciferase stability
Analysis of nucleotide diversity of NAT2 coding region reveals homogeneity across Native American populations and high intra-population diversity.

PMID 16847467 · PMC3099416 · The pharmacogenomics journal · 2007 · 8 claims · 6 setups

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NAT2 variants are homogeneously distributed across native populations of the American continent

chromosomes same inferred american pcr statistical haplotype
TM4SF10 gene sequencing in XLMR patients identifies common polymorphisms but no disease-associated mutation.

PMID 15345028 · PMC517934 · BMC medical genetics · 2004 · 8 claims · 4 setups

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No disease-associated mutations were found in TM4SF10 in 16 XLMR patients from 14 families with linkage to the TM4SF10 locus.

genomic dog sage pcr northern sage
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
In silico whole-genome screening for cancer-related single-nucleotide polymorphisms located in human mRNA untranslated regions.

PMID 17201911 · PMC1774567 · BMC genomics · 2007 · 8 claims · 5 setups

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A computational EST-based pipeline can identify UTR-SNPs that are statistically over-represented in cancerous versus normal tissue libraries

est acute 100-nt whole-genome est-based pcr-based secondary
A novel matrix metalloproteinase 2 (MMP2) terminal hemopexin domain mutation in a family with multicentric osteolysis with nodulosis and arthritis with cardiac defects.

PMID 18985071 · PMC2721823 · European journal of human genetics : EJHG · 2009 · 7 claims · 8 setups

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A novel homozygous frameshift mutation (1732delA) in exon 11 of MMP2 causes MONA in this Turkish family by deleting the terminal (third and fourth) hemopexin domains.

blood-derived patient-derived serum genomic direct rt-pcr gelatin
Stemness genes and miR-1247-3p expression associate with clinicopathological parameters and prognosis in lung adenocarcinoma.

PMID 37948380 · PMC10637681 · PloS one · 2023 · 6 claims · 7 setups

Has reproduction · 90

Three stem cell-related genes (ORC1L, KIF20A, DLGAP5) are differentially expressed in LUAD and correlate with altered immune infiltration and reduced patient survival.

luad differentially bulk mirna-seq microarray
Identification of miRNA targets with stable isotope labeling by amino acids in cell culture.

PMID 16945957 · PMC1636363 · Nucleic acids research · 2006 · 8 claims · 4 setups

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SILAC can be used for miRNA target identification

hela 3'-utr silac microarray dual-luciferase
Identification of polymorphisms and balancing selection in the male infertility candidate gene, ornithine decarboxylase antizyme 3.

PMID 16542438 · PMC1526716 · BMC medical genetics · 2006 · 8 claims · 6 setups

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Mutations in the OAZ3 gene are not a common cause of male infertility

genomic coding inferred oaz3 direct sscp haplotype
Glucocorticoid resistance in a multiple myeloma cell line is regulated by a transcription elongation block in the glucocorticoid receptor gene (NR3C1).

PMID 19133980 · PMC4303606 · British journal of haematology · 2009 · 7 claims · 6 setups

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Downregulation of GR mRNA in the resistant myeloma cell line is caused by a block to transcriptional elongation within intron B of the GR gene

mm.1s pcr demethylating quantitative

Experiments

ARED Organism: expansion of ARED reveals AU-rich element cluster variations between human and mouse.

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

Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing.

3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer.

The association of Alu repeats with the generation of potential AU-rich elements (ARE) at 3' untranslated regions.

ARED 3.0: the large and diverse AU-rich transcriptome.

Distribution and effects of nonsense polymorphisms in human genes.

Screening for microsatellite instability identifies frequent 3'-untranslated region mutation of the RB1-inducible coiled-coil 1 gene in colon tumors.

The exonuclease Xrn1 activates transcription and translation of mRNAs encoding membrane proteins.

Roar: detecting alternative polyadenylation with standard mRNA sequencing libraries.

Effects of two common polymorphisms in the 3' untranslated regions of estrogen receptor beta on mRNA stability and translatability.

Analysis of nucleotide diversity of NAT2 coding region reveals homogeneity across Native American populations and high intra-population diversity.

TM4SF10 gene sequencing in XLMR patients identifies common polymorphisms but no disease-associated mutation.

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

In silico whole-genome screening for cancer-related single-nucleotide polymorphisms located in human mRNA untranslated regions.

A novel matrix metalloproteinase 2 (MMP2) terminal hemopexin domain mutation in a family with multicentric osteolysis with nodulosis and arthritis with cardiac defects.

Stemness genes and miR-1247-3p expression associate with clinicopathological parameters and prognosis in lung adenocarcinoma.

Identification of miRNA targets with stable isotope labeling by amino acids in cell culture.

Identification of polymorphisms and balancing selection in the male infertility candidate gene, ornithine decarboxylase antizyme 3.

Glucocorticoid resistance in a multiple myeloma cell line is regulated by a transcription elongation block in the glucocorticoid receptor gene (NR3C1).