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 98

System / cell line: kinase ✕ Clear

Activation-induced cytidine deaminase acts as a mutator in BCR-ABL1-transformed acute lymphoblastic leukemia cells.

PMID 17485517 · PMC2118573 · The Journal of experimental medicine · 2007 · 8 claims · 8 setups

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AID mRNA is aberrantly expressed in Ph+ ALL but largely absent in Ph- ALL

normal ph+ semiquantitative western rt-pcr
Mutation of ERBB2 provides a novel alternative mechanism for the ubiquitous activation of RAS-MAPK in ovarian serous low malignant potential tumors.

PMID 19010816 · PMC6953412 · Molecular cancer research : MCR · 2008 · 8 claims · 8 setups

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Activating RAS-MAPK pathway mutations are present in >70% of serous LMP tumors versus ~12.5% of serous ovarian carcinomas

serous same lmp braf-mutant gene hotspot erbb2
GeneSpeed Beta Cell: an online genomics data repository and analysis resource tailored for the islet cell biologist.

PMID 18795106 · PMC2532782 · Experimental diabetes research · 2008 · 6 claims · 4 setups

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GeneSpeed Beta Cell is an online genomics data repository allowing simultaneous multiexperiment viewing and multidimensional (Boolean intersection/union) querying of pancreas- and islet-relevant datasets, integrated with GeneSpeed's domain-based gene categorization.

embryonic pancreatic panel pituitary affymetrix
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
Direct resequencing of the complete ERBB2 coding sequence reveals an absence of activating mutations in ERBB2 amplified breast cancer.

PMID 18418848 · PMC6668724 · Genes, chromosomes & cancer · 2008 · 6 claims · 5 setups

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Emulsion PCR combined with picotiter plate pyrosequencing (454 sequencing) enables high-resolution, high-throughput detection of low-frequency sequence variants among the many individual copies of an amplified gene.

erbb2-amplified erbb2-positive plasmid cos-7 emulsion serial immune-complex
Epidermal growth factor receptor structural alterations in gastric cancer.

PMID 18199332 · PMC2244615 · BMC cancer · 2008 · 8 claims · 4 setups

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EGFR structural alterations are rare in gastric carcinoma

gastric genomic direct fluorescence pcr
Phosphoproteomics by mass spectrometry: insights, implications, applications and limitations.

PMID 19929607 · PMC2931417 · Expert review of proteomics · 2009 · 8 claims · 8 setups

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Serine/threonine phosphorylation widely functions to modulate protein-protein interactions (PPIs) across signaling systems

hela jurkat exposed yeast quantitative antibody-based analog-sensitive
In vivo phosphoproteome of human skeletal muscle revealed by phosphopeptide enrichment and HPLC-ESI-MS/MS.

PMID 19764811 · PMC2783959 · Journal of proteome research · 2009 · 8 claims · 6 setups

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This is the first large-scale in vivo phosphoproteomic study of human skeletal muscle

vastus skeletal spectra identified phosphopeptide in-solution strong
Divide and conquer: progress in the molecular stratification of cancer.

PMID 19718393 · PMC2730607 · Yonsei medical journal · 2009 · 8 claims · 8 setups

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Cancers exhibit significant clinical, histopathologic, and molecular heterogeneity between individual patients

breast nsclc colon early-stage immunohistochemistry gene comparative
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
MatchMiner: a tool for batch navigation among gene and gene product identifiers.

PMID 12702208 · PMC154578 · Genome biology · 2003 · 8 claims · 3 setups

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MatchMiner's LookUp function automates batch translation of an input list of gene identifiers into a matching list of a different identifier type.

nci-60 fish-mapped random batch fish-mapped cross-validation
AutoCSA, an algorithm for high throughput DNA sequence variant detection in cancer genomes.

PMID 17485433 · PMC5947781 · Bioinformatics (Oxford, England) · 2007 · 7 claims · 2 setups

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AutoCSA is an automated algorithm, extended from the CSA protocol, that detects DNA sequence variants in cancer genomes with minimal manual intervention

training kinase capillary targeted
Quantitative phosphoproteomics by mass spectrometry: past, present, and future.

PMID 18846511 · PMC2701620 · Proteomics · 2008 · 8 claims · 6 setups

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Selective enrichment of phosphopeptides (antiphosphotyrosine IP, IMAC, TiO2/MOAC, SCX, chemical tagging) is required to detect substoichiometric, transient phosphorylation events by MS

adipocytes jurkat mammary specified antiphosphotyrosine phosphospecific comparative
Mathematical models in mammalian cell biology.

PMID 18638360 · PMC2530880 · Genome biology · 2008 · 8 claims · 8 setups

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A point mutation in the circadian Per2 gene causes familial advanced sleep phase syndrome (FASPS) via a phosphorylation defect that alters PER2 stability and subcellular localization.

culture skin hela mammalian live-cell confocal phosphoprotein
Identification of phenotype-specific networks from paired gene expression-cell shape imaging data.

PMID 35197309 · PMC8997347 · Genome research · 2022 · 8 claims · 8 setups

Has reproduction · 100

WGCNA-derived gene coexpression modules from breast cancer cell line RNA-seq data correlate significantly with specific cell-shape features

breast same gene identified bulk high-content regulon
RummaGEO: Automatic mining of human and mouse gene sets from GEO.

PMID 39569206 · PMC11573963 · Patterns (New York, N.Y.) · 2024 · 8 claims · 7 setups

Has reproduction · 63

RummaGEO is a gene expression signature search engine built from automatically mined human and mouse RNA-seq perturbation studies in GEO

genes rummageo rummageo-derived leiden bulk gene leiden
GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets.

PMID 40208796 · PMC11984350 · GigaScience · 2025 · 8 claims · 8 setups

Has reproduction · 76

GeneSetCart is a web-based platform that lets users assemble, augment, combine, visualize, and analyze gene sets from multiple sources in one place

user-assembled archs4 generif-derived aggregated gene gene-gene literature
Molecular genetic analysis of an endotoxin nonresponder mutant cell line: a point mutation in a conserved region of MD-2 abolishes endotoxin-induced signaling.

PMID 11435474 · PMC2193443 · The Journal of experimental medicine · 2001 · 8 claims · 7 setups

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MD-2 is a required component of the LPS signaling complex; a point mutation in MD-2 abolishes LPS-induced signaling

cho hek western nf-kb il-6
The cohesin complex: sequence homologies, interaction networks and shared motifs.

PMID 11276426 · PMC30708 · Genome biology · 2001 · 8 claims · 8 setups

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Mouse Mmip1 and Smc3 (SMCD) share 99% sequence identity and are products of the same gene

smc1 smc3 mmip1 smc psi-blast phylogenetic sequence
A Korean family with Arg1448Cys mutation of SCN4A channel causing paramyotonia congenita: electrophysiologic, histopathologic, and molecular genetic studies.

PMID 12483017 · PMC3054970 · Journal of Korean medical science · 2002 · 7 claims · 5 setups

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A missense mutation (Arg1448Cys, R1448C) in SCN4A causes paramyotonia congenita in this Korean family

skeletal abductor genomic proband needle short muscle

Experiments

Activation-induced cytidine deaminase acts as a mutator in BCR-ABL1-transformed acute lymphoblastic leukemia cells.

Mutation of ERBB2 provides a novel alternative mechanism for the ubiquitous activation of RAS-MAPK in ovarian serous low malignant potential tumors.

GeneSpeed Beta Cell: an online genomics data repository and analysis resource tailored for the islet cell biologist.

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.

Direct resequencing of the complete ERBB2 coding sequence reveals an absence of activating mutations in ERBB2 amplified breast cancer.

Epidermal growth factor receptor structural alterations in gastric cancer.

Phosphoproteomics by mass spectrometry: insights, implications, applications and limitations.

In vivo phosphoproteome of human skeletal muscle revealed by phosphopeptide enrichment and HPLC-ESI-MS/MS.

Divide and conquer: progress in the molecular stratification of cancer.

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

MatchMiner: a tool for batch navigation among gene and gene product identifiers.

AutoCSA, an algorithm for high throughput DNA sequence variant detection in cancer genomes.

Quantitative phosphoproteomics by mass spectrometry: past, present, and future.

Mathematical models in mammalian cell biology.

Identification of phenotype-specific networks from paired gene expression-cell shape imaging data.

RummaGEO: Automatic mining of human and mouse gene sets from GEO.

GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets.

Molecular genetic analysis of an endotoxin nonresponder mutant cell line: a point mutation in a conserved region of MD-2 abolishes endotoxin-induced signaling.

The cohesin complex: sequence homologies, interaction networks and shared motifs.

A Korean family with Arg1448Cys mutation of SCN4A channel causing paramyotonia congenita: electrophysiologic, histopathologic, and molecular genetic studies.