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 45

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

Genomic and transcriptomic plasticity in treatment-naive ovarian cancer.

PMID 24221193 · PMC3912411 · Genome research · 2014 · 8 claims · 8 setups

Has reproduction · 30

Treatment-naïve epithelial ovarian cancers show extensive intra-tumor heterogeneity of genomic rearrangements, with the most substantial differences occurring between omentum/peritoneum metastases and ovarian tumor sites.

tumor each rna-seq whole-genome targeted pcr-based
Complex landscapes of somatic rearrangement in human breast cancer genomes.

PMID 20033038 · PMC3398135 · Nature · 2009 · 8 claims · 6 setups

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There are more somatic rearrangements in some breast cancers than previously appreciated by cytogenetic methods.

breast subset confirmed paired-end fish exon-exon
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
Molecular genetic diagnosis of von Hippel-Lindau disease: analysis of five Japanese families.

PMID 8641976 · PMC5921130 · Japanese journal of cancer research : Gann · 1996 · 5 claims · 3 setups

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Four of five Japanese VHL disease families showed germ line VHL gene mutations, comprising 2 missense mutations, 1 deletion, and 1 splice-site mutation

blood-derived hemangioblastoma single-strand direct sscp
Prevalence and clinical correlates of JAK2 mutations in Down syndrome acute lymphoblastic leukaemia.

PMID 19120350 · PMC2724897 · British journal of haematology · 2009 · 8 claims · 4 setups

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JAK2 R683 point mutations occur in 18.9% (10/53) of DS ALL cases, confirming the previously reported incidence.

bone remission sanger pyrosequencing paired
Somatic mutation of epidermal growth factor receptor in a small subset of cutaneous squamous cell carcinoma.

PMID 19812598 · PMC2825112 · The Journal of investigative dermatology · 2010 · 8 claims · 5 setups

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EGFR is activated by somatic mutation in a small subset of cutaneous SCC

archival scc sanger array-based fluorescence
Computationally scalable regression modeling for ultrahigh-dimensional omics data with ParProx.

PMID 34254998 · PMC8575036 · Briefings in bioinformatics · 2021 · 6 claims · 4 setups

Has reproduction · 79

ParProx implements overlapping and non-overlapping (latent) group lasso regression for time-to-event (Cox) and classification (logistic) analysis with variables grouped by biological priors.

tcga breast liver synthetic somatic gene methylation-based
Screening for TP53 mutations in patients and tumours from 109 Swedish breast cancer families.

PMID 9099970 · PMC2222784 · British journal of cancer · 1997 · 6 claims · 6 setups

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No germline TP53 mutations (exons 5-8) were found in 128 breast cancer patients from 109 families with familial cancer.

genomic tumour paired constant restriction sequencing
Somatic VHL gene alterations in MEN2-associated medullary thyroid carcinoma.

PMID 16707008 · PMC1483898 · BMC cancer · 2006 · 6 claims · 4 setups

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Somatic VHL gene alterations (LOH and mutation) may contribute to pathogenesis of MEN2A-associated MTC, similar to their role in MEN2 pheochromocytoma

microdissected same genomic frozen microsatellite loss vhl
Comprehensive genomic analysis reveals clinically relevant molecular distinctions between thymic carcinomas and thymomas.

PMID 19861435 · PMC2783876 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 7 claims · 7 setups

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Comprehensive genomic analysis shows thymic carcinomas are molecularly distinct from thymomas

resected thymic previously mass dideoxynucleotide array
Absence of somatic alterations of the EB1 gene adenomatous polyposis coli-associated protein in human sporadic colorectal cancers.

PMID 9823979 · PMC2063196 · British journal of cancer · 1998 · 6 claims · 4 setups

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No somatic point mutations were found in the entire EB1 coding sequence in sporadic colorectal cancers or adenomas

sporadic pcr colorectal rt-pcr direct microsatellite
Genomic and mutational profiling to assess clonal relationships between multiple non-small cell lung cancers.

PMID 19671847 · PMC2892178 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 8 claims · 5 setups

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Genomic profiling by aCGH can distinguish clonal tumors from independent primaries with high confidence by identifying matching versus non-matching regions of allelic gain/loss.

fresh-frozen same banked resected array mutational pcr
Loss or somatic mutations of hMSH2 occur in hereditary nonpolyposis colorectal cancers with hMSH2 germline mutations.

PMID 8613431 · PMC5921088 · Japanese journal of cancer research : Gann · 1996 · 5 claims · 4 setups

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hMSH2 germline mutations were detected in 5 of 36 Japanese HNPCC kindreds (14%)

peripheral tumor sscp somatic loss
DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.

PMID 18987736 · PMC2603574 · Nature · 2008 · 8 claims · 8 setups

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Whole genome sequencing can identify unbiased, novel somatic mutations in a cytogenetically normal AML genome that would not have been found by candidate-gene resequencing.

aml tumor novo additional genome snp comparative
Mutation analysis in primary immunodeficiency diseases: case studies.

PMID 19841577 · PMC2774237 · Current opinion in allergy and clinical immunology · 2009 · 8 claims · 8 setups

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Genomic DNA Sanger sequencing is the standard first-line approach for identifying PIDD-causing mutations but has limitations that can yield false-negative or false-positive results

mother parents ebv-transformed nemo genomic flow northern
Prevalence and functional analysis of sequence variants in the ATR checkpoint mediator Claspin.

PMID 19737971 · PMC2994259 · Molecular cancer research : MCR · 2009 · 8 claims · 8 setups

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CLSPN is a mediator protein essential for the ATR- and CHK1-dependent checkpoint response to replicative stress or single-stranded DNA

ebv-immortalized sporadic same caucasian genomic denaturing genotyping
COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer.

PMID 19906727 · PMC2808858 · Nucleic acids research · 2010 · 8 claims · 6 setups

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COSMIC is the largest public resource for information on somatically acquired mutations in human cancer, freely available without restriction

cancer tumour manual semi-automated candidate
Analysis of the TGF beta functional pathway in epithelial ovarian carcinoma.

PMID 11531253 · PMC2364123 · British journal of cancer · 2001 · 6 claims · 6 setups

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IGFIIR, TGFβ1 and TGFβRII are proposed to function as a unit in the TGFβ growth inhibitory pathway

epithelial tumor genomic ovarian sscp sequencing pcr
Identification and characterisation of the angiotensin converting enzyme-3 (ACE3) gene: a novel mammalian homologue of ACE.

PMID 17597519 · PMC1925091 · BMC genomics · 2007 · 7 claims · 7 setups

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A novel single-domain ACE-like gene, ACE3, exists in mouse, rat, cow, dog and human genomes, located on the same chromosome downstream of ACE.

dog predicted ace3 panel blast sequence homology
Lack of involvement of known DNA methyltransferases in familial hydatidiform mole implies the involvement of other factors in establishment of imprinting in the human female germline.

PMID 12546714 · PMC149328 · BMC genetics · 2003 · 8 claims · 5 setups

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A human oocyte-specific DNMT1 isoform (DNMT1o), driven by a novel upstream exon 1o, is expressed in mature oocytes and early embryos but not in somatic tissues

oocytes genomic fbhm population rt-pcr est direct

Experiments

Genomic and transcriptomic plasticity in treatment-naive ovarian cancer.

Complex landscapes of somatic rearrangement in human breast cancer genomes.

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

Molecular genetic diagnosis of von Hippel-Lindau disease: analysis of five Japanese families.

Prevalence and clinical correlates of JAK2 mutations in Down syndrome acute lymphoblastic leukaemia.

Somatic mutation of epidermal growth factor receptor in a small subset of cutaneous squamous cell carcinoma.

Computationally scalable regression modeling for ultrahigh-dimensional omics data with ParProx.

Screening for TP53 mutations in patients and tumours from 109 Swedish breast cancer families.

Somatic VHL gene alterations in MEN2-associated medullary thyroid carcinoma.

Comprehensive genomic analysis reveals clinically relevant molecular distinctions between thymic carcinomas and thymomas.

Absence of somatic alterations of the EB1 gene adenomatous polyposis coli-associated protein in human sporadic colorectal cancers.

Genomic and mutational profiling to assess clonal relationships between multiple non-small cell lung cancers.

Loss or somatic mutations of hMSH2 occur in hereditary nonpolyposis colorectal cancers with hMSH2 germline mutations.

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.

Mutation analysis in primary immunodeficiency diseases: case studies.

Prevalence and functional analysis of sequence variants in the ATR checkpoint mediator Claspin.

COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer.

Analysis of the TGF beta functional pathway in epithelial ovarian carcinoma.

Identification and characterisation of the angiotensin converting enzyme-3 (ACE3) gene: a novel mammalian homologue of ACE.

Lack of involvement of known DNA methyltransferases in familial hydatidiform mole implies the involvement of other factors in establishment of imprinting in the human female germline.