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 38

System / cell line: genomic ✕ Assay: immunoprecipitation ✕ Clear

CDKN2A and CDK4 mutation analysis in Italian melanoma-prone families: functional characterization of a novel CDKN2A germ line mutation.

PMID 11556834 · PMC2375081 · British journal of cancer · 2001 · 7 claims · 6 setups

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Germ line CDKN2A mutations were found in 5 of 15 (33.3%) Italian melanoma-prone families, including one novel mutation (P48T) and three known pathogenic mutations (R24P, G101W, N71S)

genomic radiolabelled tig-er u2os sscp protein-protein retroviral
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
Functional effects of KCNE3 mutation and its role in the development of Brugada syndrome.

PMID 19122847 · PMC2585750 · Circulation. Arrhythmia and electrophysiology · 2008 · 7 claims · 5 setups

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A missense R99H mutation in KCNE3 was identified in a Brugada Syndrome proband and cosegregates with the phenotype in the family (4/4 phenotype-positive, 0/3 phenotype-negative members carried it)

genomic cho-k1 left ventricular sscp whole-cell co-immunoprecipitation
A novel breast cancer-associated BRIP1 (FANCJ/BACH1) germ-line mutation impairs protein stability and function.

PMID 18628483 · PMC2561321 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2008 · 6 claims · 7 setups

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A novel heterozygous BRIP1 germline mutation (c.2992-2995delAAGA) was identified in a breast cancer patient, causing a frameshift and premature stop codon in exon 20.

genomic laser-capture cell-free hela sscp loss transcription
PReMod: a database of genome-wide mammalian cis-regulatory module predictions.

PMID 17148480 · PMC1761432 · Nucleic acids research · 2007 · 8 claims · 3 setups

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PReMod is a database of genome-wide predicted cis-regulatory modules (pCRMs) for the human and mouse genomes.

genome chip-chip comparative
Extent of laminin-5 assembly and secretion effect junctional epidermolysis bullosa phenotype.

PMID 9547338 · PMC2212220 · The Journal of experimental medicine · 1998 · 6 claims · 6 setups

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The most severe (Herlitz) form of JEB correlates best with mutations causing premature termination codons (PTCs), not with mutation location in a particular protein domain

keratinocytes keratinocyte genomic pcr biosynthetic northern pcr
High-throughput molecular analysis in lung cancer: insights into biology and potential clinical applications.

PMID 19648524 · PMC4648268 · The European respiratory journal · 2009 · 8 claims · 8 setups

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High-throughput -omics technologies have revolutionised understanding of lung cancer biology and hold promise for personalised management of lung cancer

tumour serum nsclc comparative snp methylation
A common polymorphism in the oxygen-dependent degradation (ODD) domain of hypoxia inducible factor-1alpha (HIF-1alpha) does not impair Pro-564 hydroxylation.

PMID 14521712 · PMC212228 · Molecular cancer · 2003 · 6 claims · 5 setups

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Pro582Ser is a common HIF-1α ODD-domain polymorphism occurring at similar frequency in idiopathic erythrocytosis patients (0.109) and normal controls (0.073)

genomic recombinant 35s-labeled sanger pcr-rflp gst
Collagen VI glycine mutations: perturbed assembly and a spectrum of clinical severity.

PMID 18825676 · PMC2743946 · Annals of neurology · 2008 · 8 claims · 6 setups

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All eight new patients had heterozygous glycine substitution mutations toward the N-terminal end of the collagen VI triple helix

dermal skeletal fibroblast confluent rt-pcr immunohistochemistry biosynthetic
Determination of Ras-GTP and Ras-GDP in patients with acute myelogenous leukemia (AML), myeloproliferative syndrome (MPS), juvenile myelomonocytic leukemia (JMML), acute lymphocytic leukemia (ALL), and malignant lymphoma: assessment of mutational and indirect activation.

PMID 18784923 · PMC2755762 · Annals of hematology · 2009 · 6 claims · 4 setups

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A non-radioactive, enzyme-coupled luminometric assay can quantify Ras activation as %GTP/(GTP+GDP) with high sensitivity (detects 1 fmol GTP)

bone n=23 3t3 ras genomic
Somatic mutations of the Parkinson's disease-associated gene PARK2 in glioblastoma and other human malignancies.

PMID 19946270 · PMC4002225 · Nature genetics · 2010 · 8 claims · 8 setups

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PARK2 is a frequently and specifically targeted gene within recurrent 6q25.2-q27 copy number losses in glioblastoma and colon cancer

colon gbm cancer dbtrg array pcr colony
52-kD SS-A/Ro: genomic structure and identification of an alternatively spliced transcript encoding a novel leucine zipper-minus autoantigen expressed in fetal and adult heart.

PMID 7561701 · PMC2192297 · The Journal of experimental medicine · 1995 · 7 claims · 7 setups

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The 52-kD SS-A/Ro gene spans 10 kb of DNA and is composed of seven exons, with the translation initiation codon in exon 2 and the leucine zipper encoded by exon 4.

molt-4 placental placenta fetal cdna genomic race
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

PMID 22955991 · PMC3431496 · Genome research · 2012 · 8 claims · 8 setups

Has reproduction · 74

ENCODE/modENCODE define a set of working standards and guidelines for ChIP-seq covering antibody validation, experimental replication, sequencing depth, data/metadata reporting, and data quality assessment.

small-genome nuclear whole-cell encode chip-seq chip-chip immunoblot
An integrated database of genes responsive to the Myc oncogenic transcription factor: identification of direct genomic targets.

PMID 14519204 · PMC328458 · Genome biology · 2003 · 8 claims · 6 setups

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The Myc Target Gene database integrates literature evidence to prioritize candidate Myc-responsive genes and cluster them into functional groups

p493 rodent types quantitative chromatin northern
Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results.

PMID 15608239 · PMC539999 · Nucleic acids research · 2005 · 8 claims · 8 setups

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GALA is now a set of interlinked relational databases covering five vertebrate species: human, chimpanzee, mouse, rat and chicken.

chromosome genomic comparative phylohmmcons conserved
Rbfox2 controls autoregulation in RNA-binding protein networks.

PMID 24637117 · PMC3967051 · Genes & development · 2014 · 8 claims · 8 setups

Has reproduction · 48

Rbfox2 cross-regulates AS-NMD events within RNA-binding protein genes to alter their expression, tuning autoregulatory splicing networks and placing Rbfox2 at a critical node of a multilayer regulatory network.

v6.5 fhfox2 top introns iclip sequencing rt-pcr
Methods for genome-wide analysis of DNA methylation in intestinal tumors.

PMID 19854208 · PMC2891386 · Mutation research · 2010 · 8 claims · 8 setups

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Aberrant DNA methylation, including CpG island hypermethylation of tumor suppressors and genome-wide hypomethylation, is strongly linked to the origin and progression of colorectal cancer.

cd19+ lung gpx1 tumor mira medip goldengate
Evaluation of genome-wide chromatin library of Stat5 binding sites in human breast cancer.

PMID 15686596 · PMC549029 · Molecular cancer · 2005 · 8 claims · 5 setups

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A chromatin library coupled with experimental validation can productively identify novel in vivo Stat5 chromatin binding sites in cancer, including abnormal regulatory sites in tumor-specific neochromatin.

t-47d agarose chromatin cloning
CHEK2 mutations affecting kinase activity together with mutations in TP53 indicate a functional pathway associated with resistance to epirubicin in primary breast cancer.

PMID 18725978 · PMC2518116 · PloS one · 2008 · 7 claims · 6 setups

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TP53 mutations, especially those affecting the L2/L3 DNA-binding domains, are associated with resistance (progressive disease) to epirubicin therapy

snap-frozen tumor u-2-os patients pcr bisulphite loss
An attenuated phenotype of Costello syndrome in three unrelated individuals with a HRAS c.179G>A (p.Gly60Asp) mutation correlates with uncommon functional consequences.

PMID 25914166 · PMC4830354 · American journal of medical genetics. Part A · 2015 · 7 claims · 8 setups

Has reproduction

HRAS c.179G>A (p.Gly60Asp) causes an attenuated Costello syndrome phenotype without severe failure-to-thrive, intellectual disability, or cancer predisposition

cos-7 transiently patients parental ras co-immunoprecipitation immunoblotting

Experiments

CDKN2A and CDK4 mutation analysis in Italian melanoma-prone families: functional characterization of a novel CDKN2A germ line mutation.

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

Functional effects of KCNE3 mutation and its role in the development of Brugada syndrome.

A novel breast cancer-associated BRIP1 (FANCJ/BACH1) germ-line mutation impairs protein stability and function.

PReMod: a database of genome-wide mammalian cis-regulatory module predictions.

Extent of laminin-5 assembly and secretion effect junctional epidermolysis bullosa phenotype.

High-throughput molecular analysis in lung cancer: insights into biology and potential clinical applications.

A common polymorphism in the oxygen-dependent degradation (ODD) domain of hypoxia inducible factor-1alpha (HIF-1alpha) does not impair Pro-564 hydroxylation.

Collagen VI glycine mutations: perturbed assembly and a spectrum of clinical severity.

Determination of Ras-GTP and Ras-GDP in patients with acute myelogenous leukemia (AML), myeloproliferative syndrome (MPS), juvenile myelomonocytic leukemia (JMML), acute lymphocytic leukemia (ALL), and malignant lymphoma: assessment of mutational and indirect activation.

Somatic mutations of the Parkinson's disease-associated gene PARK2 in glioblastoma and other human malignancies.

52-kD SS-A/Ro: genomic structure and identification of an alternatively spliced transcript encoding a novel leucine zipper-minus autoantigen expressed in fetal and adult heart.

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

An integrated database of genes responsive to the Myc oncogenic transcription factor: identification of direct genomic targets.

Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results.

Rbfox2 controls autoregulation in RNA-binding protein networks.

Methods for genome-wide analysis of DNA methylation in intestinal tumors.

Evaluation of genome-wide chromatin library of Stat5 binding sites in human breast cancer.

CHEK2 mutations affecting kinase activity together with mutations in TP53 indicate a functional pathway associated with resistance to epirubicin in primary breast cancer.

An attenuated phenotype of Costello syndrome in three unrelated individuals with a HRAS c.179G>A (p.Gly60Asp) mutation correlates with uncommon functional consequences.