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 36

System / cell line: utr ✕ Assay: exon ✕ Clear

CEAS: cis-regulatory element annotation system.

PMID 16845068 · PMC1538818 · Nucleic acids research · 2006 · 7 claims · 5 setups

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CEAS is the first web server to streamline genome-scale ChIP-chip downstream analyses for biologists without strong bioinformatics support

genome genomic chip-chip repeat-masked conservation
Large-scale analysis of Macaca fascicularis transcripts and inference of genetic divergence between M. fascicularis and M. mulatta.

PMID 18294402 · PMC2287170 · BMC genomics · 2008 · 8 claims · 6 setups

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Constructed full-length-enriched cDNA libraries and determined 85,721 EST sequences and 9407 full-insert sequences from cynomolgus macaque brain (7 regions), testis, and liver

cynomolgus 3-year-old macaque est full-insert oligonucleotide
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
HITS-CLIP yields genome-wide insights into brain alternative RNA processing.

PMID 18978773 · PMC2597294 · Nature · 2008 · 8 claims · 8 setups

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HITS-CLIP, combining CLIP with high-throughput sequencing, provides a genome-wide, unbiased method to map protein-RNA interactions in vivo.

neocortex brain 293t hits-clip traditional exon
Genetic variation at hair length candidate genes in elephants and the extinct woolly mammoth.

PMID 19747392 · PMC2754481 · BMC evolutionary biology · 2009 · 8 claims · 5 setups

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The coding sequence of FGF5 is not the critical determinant of hair length differences among elephantids, including the woolly mammoth.

asian fgf5 woolly savanna pcr structural blast
JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions.

PMID 16925843 · PMC1810558 · Genome biology · 2006 · 8 claims · 4 setups

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Adding model states for specific biological features (signal peptides, CpG islands, etc.) to non-comparative GHMM gene finders did little or nothing to enhance predictive accuracy, sometimes reducing it.

encode genes invertebrate initio comparative training
Alternative splicing of human peroxisome proliferator-activated receptor delta (PPAR delta): effects on translation efficiency and trans-activation ability.

PMID 17705821 · PMC2045109 · BMC molecular biology · 2007 · 8 claims · 8 setups

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Multiple alternatively spliced 5'-UTR isoforms of human PPARdelta mRNA differ in translation efficiency

placenta five lines huh7 5'-race rt-pcr real-time
Association between the ACCN1 gene and multiple sclerosis in Central East Sardinia.

PMID 17534430 · PMC1868958 · PloS one · 2007 · 8 claims · 6 setups

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Microsatellite D17S798 in the 17q11.2 region shows significant association with MS

nuclear accn1 genetic genotype microsatellite direct snp
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
Expanding CEP290 mutational spectrum in ciliopathies.

PMID 19764032 · PMC4340070 · American journal of medical genetics. Part A · 2009 · 7 claims · 4 setups

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A large heterozygous genomic deletion spanning the CEP290 C-terminus (exons 42-54) was identified in a JSRD-COR patient previously known to carry only one CEP290 point mutation.

peripheral genomic quantitative cdna pcr
Two novel missense mutations in the myostatin gene identified in Japanese patients with Duchenne muscular dystrophy.

PMID 17428346 · PMC1855920 · BMC medical genetics · 2007 · 7 claims · 5 setups

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Two novel missense mutations in the myostatin gene (p.95D>H and p.156L>I) were identified in Japanese DMD patients

genomic pcr elbow peripheral pcr subcloning gel
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
Organismal complexity, cell differentiation and gene expression: human over mouse.

PMID 17881362 · PMC2095826 · Nucleic acids research · 2007 · 8 claims · 7 setups

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Human shows a greater fraction of tissue-specific genes and a greater ratio of total expression of tissue-specific to housekeeping genes than mouse across 32 homologous tissues

human-mouse oligonucleotide exon comparative
Mutational hot spot potential of a novel base pair mutation of the CSPG2 gene in a family with Wagner syndrome.

PMID 19901218 · PMC3514888 · Archives of ophthalmology (Chicago, Ill. : 1960) · 2009 · 8 claims · 4 setups

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No COL2A1 mutations were found, making ocular Stickler syndrome an unlikely diagnosis for this family

genomic family complete pcr clinical
Constitutive RB1 mutation in a child conceived by in vitro fertilization: implications for genetic counseling.

PMID 19640284 · PMC2726130 · BMC medical genetics · 2009 · 7 claims · 4 setups

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The retinoblastoma proband carries a novel constitutive RB1 mutation (g.2056C>G) at position -4 of the 5'UTR Kozak consensus sequence, absent in her father and unaffected sisters

genomic proband's pcr rt-pcr multiplex
Detection of mutations in the dystrophin gene via automated DHPLC screening and direct sequencing.

PMID 11710958 · PMC59832 · BMC genetics · 2001 · 7 claims · 6 setups

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DHPLC screening combined with direct sequencing detects likely disease-causative point mutations in the dystrophin gene missed by multiplexed PCR deletion/duplication testing

genomic muscle blood direct dhplc multiplexed
Human CCS gene: genomic organization and exclusion as a candidate for amyotrophic lateral sclerosis (ALS).

PMID 11991808 · PMC107843 · BMC genetics · 2002 · 6 claims · 5 setups

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The genomic organization of human CCS was characterized, with the 823 bp coding region organized into 8 exons spanning 12798 bp of genomic DNA.

bac heart ccs genomic genomic rt-pcr transcription
Speeding disease gene discovery by sequence based candidate prioritization.

PMID 15766383 · PMC1274252 · BMC bioinformatics · 2005 · 7 claims · 8 setups

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Disease genes (OMIM) differ significantly from non-disease genes in sequence-based features including gene/cDNA/protein size, exon number, homolog conservation, secretion signal, 3' UTR length, CpG islands, and distance to nearest gene.

ensembl training same hgmd comparative machine tenfold
Screening of the transcriptional regulatory regions of vascular endothelial growth factor receptor 2 (VEGFR2) in amyotrophic lateral sclerosis.

PMID 17456229 · PMC1868706 · BMC medical genetics · 2007 · 7 claims · 4 setups

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No mutations were identified in the VEGFR2 gene (exons 7, 18, 21, 27, promoter, or 5' UTR) in ALS patients

genomic pcr als direct restriction allele
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

CEAS: cis-regulatory element annotation system.

Large-scale analysis of Macaca fascicularis transcripts and inference of genetic divergence between M. fascicularis and M. mulatta.

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.

HITS-CLIP yields genome-wide insights into brain alternative RNA processing.

Genetic variation at hair length candidate genes in elephants and the extinct woolly mammoth.

JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions.

Alternative splicing of human peroxisome proliferator-activated receptor delta (PPAR delta): effects on translation efficiency and trans-activation ability.

Association between the ACCN1 gene and multiple sclerosis in Central East Sardinia.

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

Expanding CEP290 mutational spectrum in ciliopathies.

Two novel missense mutations in the myostatin gene identified in Japanese patients with Duchenne muscular dystrophy.

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

Organismal complexity, cell differentiation and gene expression: human over mouse.

Mutational hot spot potential of a novel base pair mutation of the CSPG2 gene in a family with Wagner syndrome.

Constitutive RB1 mutation in a child conceived by in vitro fertilization: implications for genetic counseling.

Detection of mutations in the dystrophin gene via automated DHPLC screening and direct sequencing.

Human CCS gene: genomic organization and exclusion as a candidate for amyotrophic lateral sclerosis (ALS).

Speeding disease gene discovery by sequence based candidate prioritization.

Screening of the transcriptional regulatory regions of vascular endothelial growth factor receptor 2 (VEGFR2) in amyotrophic lateral sclerosis.

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