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 14

System / cell line: cases ✕ Assay: fisher ✕ Clear

Combinatorial Mismatch Scan (CMS) for loci associated with dementia in the Amish.

PMID 16515697 · PMC1448207 · BMC medical genetics · 2006 · 8 claims · 7 setups

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CMS compares IBS allele/genotype sharing between distantly related (beyond grandparental) affected and unaffected individuals from founder populations to detect disease loci while reducing confounding from population stratification and genetic heterogeneity.

amish unrelated same overall microsatellite combinatorial permutation
Screening large-scale association study data: exploiting interactions using random forests.

PMID 15588316 · PMC545646 · BMC genetics · 2004 · 7 claims · 3 setups

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Random forest importance measure significantly outperforms the Fisher Exact test as a screening tool when risk SNPs interact.

simulated same simulation random fisher
PALB2 variants in hereditary and unselected Finnish prostate cancer cases.

PMID 20003494 · PMC2806404 · Journal of negative results in biomedicine · 2009 · 8 claims · 6 setups

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None of the detected PALB2 variants, including 1592delT, show significant association with PRCA at the population level in Finland

blood finnish combined formalin-fixed direct additional statistical
Interaction between two independent CNR1 variants increases risk for cocaine dependence in European Americans: a replication study in family-based sample and population-based sample.

PMID 19052543 · PMC2879626 · Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2009 · 8 claims · 8 setups

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The interaction between SNP3^G+ genotypes and SNP8^T/T genotype significantly increases risk for cocaine dependence in EA family and EA case-control samples.

family case-control pooled unrelated snp family-based case-control
Missense polymorphisms in the adenomatous polyposis coli gene and colorectal cancer risk.

PMID 18612690 · PMC2768068 · Diseases of the colon and rectum · 2008 · 7 claims · 4 setups

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Germline missense APC alterations (S130G, E1317Q, D1822V, G2502S) identified in a CRC-multiple-polyp cohort do not confer significantly increased CRC risk when tested in a large population-based case-control series

germline same population-based ofccr manual dhplc nuclease
Calibrating the performance of SNP arrays for whole-genome association studies.

PMID 18584036 · PMC2432039 · PLoS genetics · 2008 · 8 claims · 7 setups

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Previous SNP array genetic coverage estimates are inflated due to SNP overfitting and sample overfitting, since they were evaluated on the same HapMap SNPs/individuals used to design the arrays.

american liver simulated hapmap snp gene simulation-based
Somatic mutations of KIT in familial testicular germ cell tumours.

PMID 15150569 · PMC2410291 · British journal of cancer · 2004 · 6 claims · 3 setups

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No germline KIT mutations were found in constitutional DNA from 240 familial TGCT pedigrees

blood ffpe familial csge direct contingency
Mutant, wild type, or overall p53 expression: freedom from clinical progression in tumours of astrocytic lineage.

PMID 15494720 · PMC2409947 · British journal of cancer · 2004 · 8 claims · 7 setups

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Significant overexpression of p53 protein was found in 48% of 74 astrocytic tumours

archival subset recombinant same immunohistochemistry antibody cytokeratin
Polymorphism screening and haplotype analysis of the tryptophan hydroxylase gene (TPH1) and association with bipolar affective disorder in Taiwan.

PMID 15799788 · PMC1079843 · BMC medical genetics · 2005 · 8 claims · 7 setups

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Systematic screening of TPH1 exons and promoter region in Taiwanese Han identified five sequence variants: A-1067G, G-347T, T3804A, C27224T, A27237G.

taiwanese bpd bess arms multiplex
BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.

PMID 16845052 · PMC1538844 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Babelomics is presented as an updated, complete suite of web tools for functional analysis of genome-scale experiments with new and improved modules

pre-selected pre-tabulated genes ranked kegg expression text-mining
Mutation screen and association studies in the diacylglycerol O-acyltransferase homolog 2 gene (DGAT2), a positional candidate gene for early onset obesity on chromosome 11q13.

PMID 17477860 · PMC1871603 · BMC genetics · 2007 · 7 claims · 5 setups

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DGAT2 is a plausible positional and functional candidate gene for obesity due to its localization at chr.11q13 (a linkage region) and its key role in triglyceride synthesis

extremely families genome sanger case-control family-based
Polymorphisms in COL4A3 and COL4A4 genes associated with keratoconus.

PMID 20029656 · PMC2796875 · Molecular vision · 2009 · 6 claims · 5 setups

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No disease-causing mutations in COL4A3 or COL4A4 were found to be related to KC.

genomic patients pcr sequencing genetic
Mutation analysis of the AATF gene in breast cancer families.

PMID 20025740 · PMC2806411 · BMC cancer · 2009 · 6 claims · 6 setups

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No AATF sequence alteration identified was predicted to be pathogenic or showed significant association with breast cancer risk

genomic showing aatf case conformation direct pathogenicity
Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival.

PMID 18778477 · PMC2553089 · BMC medicine · 2008 · 7 claims · 7 setups

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A custom BOAC SNP panel of 3404 SNPs in 983 genes was developed using the Affymetrix GeneChip Targeted Genotyping Platform, focused on non-synonymous coding SNPs and regulatory-region SNPs in candidate genes.

coriell myeloma duplicate snp targeted genotyping machine

Experiments

Combinatorial Mismatch Scan (CMS) for loci associated with dementia in the Amish.

Screening large-scale association study data: exploiting interactions using random forests.

PALB2 variants in hereditary and unselected Finnish prostate cancer cases.

Interaction between two independent CNR1 variants increases risk for cocaine dependence in European Americans: a replication study in family-based sample and population-based sample.

Missense polymorphisms in the adenomatous polyposis coli gene and colorectal cancer risk.

Calibrating the performance of SNP arrays for whole-genome association studies.

Somatic mutations of KIT in familial testicular germ cell tumours.

Mutant, wild type, or overall p53 expression: freedom from clinical progression in tumours of astrocytic lineage.

Polymorphism screening and haplotype analysis of the tryptophan hydroxylase gene (TPH1) and association with bipolar affective disorder in Taiwan.

BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.

Mutation screen and association studies in the diacylglycerol O-acyltransferase homolog 2 gene (DGAT2), a positional candidate gene for early onset obesity on chromosome 11q13.

Polymorphisms in COL4A3 and COL4A4 genes associated with keratoconus.

Mutation analysis of the AATF gene in breast cancer families.

Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival.