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).

• Association of GSK3B with Alzheimer disease and frontotemporal dementia.

  PMID 18852354 · PMC2841136 · Archives of neurology · 2008 · 8 claims · 5 setups

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  The GSK3B intronic polymorphism IVS2-68G>A is associated with increased risk of AD and FTD in a case-control cohort

  genomic case-control family-based sib-pair pcr allele-specific fluorescence-polarization

• 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

• VEGF, FGF1, FGF2 and EGF gene polymorphisms and psoriatic arthritis.

  PMID 17204151 · PMC1781940 · BMC musculoskeletal disorders · 2007 · 7 claims · 5 setups

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  The T allele of VEGF +936 (rs3025039) is significantly less frequent in PsA cases than in controls, suggesting a protective effect against PsA.

  blood same subject psa snp allele hardy-weinberg

• Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.

  PMID 18515841 · PMC2447758 · Nucleic acids research · 2008 · 8 claims · 5 setups

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  Babelomics is a web suite offering both conventional functional enrichment methods and more advanced gene set analysis (GSA) methods, a combination offered by only one other tool (FuncAssociate) among competitors.

  user-supplied ranked gene fasta-formatted functional gene novo

• Gene- and evidence-based candidate gene selection for schizophrenia and gene feature analysis.

  PMID 19944577 · PMC2826526 · Artificial intelligence in medicine · 2010 · 8 claims · 5 setups

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  The SCOR method outperforms the CCOR method for prioritizing schizophrenia candidate genes

  schizophrenia genes ranked gene-based gene expression

• Single nucleotide polymorphisms of the APC gene and colorectal cancer risk: a case-control study in Taiwan.

  PMID 16569251 · PMC1488868 · BMC cancer · 2006 · 7 claims · 4 setups

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  Three novel APC germline mutations were identified in Taiwanese subjects: a frameshift deletion at codon 460 (g.1378delG), and two missense substitutions p.V1125A and p.S1126R

  genomic taiwanese dhplc pcr sanger

• 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

• HFE H63D mutation frequency shows an increase in Turkish women with breast cancer.

  PMID 16503999 · PMC1402308 · BMC cancer · 2006 · 6 claims · 2 setups

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  HFE H63D allele frequency is significantly higher in Turkish breast cancer patients (22.2%) than in healthy controls (14%)

  archived same pcr-rflp 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

• The association of membrane frizzled-related protein (MFRP) gene with acute angle-closure glaucoma--a pilot study.

  PMID 18781223 · PMC2532703 · Molecular vision · 2008 · 8 claims · 4 setups

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  None of the three MFRP sequence variants tested (rs3814762, rs36015759, rs2510143) showed a statistically significant association with acute angle-closure glaucoma

  genomic same eyes pcr genotype linkage

• 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

• Association of HFE common mutations with Parkinson's disease, Alzheimer's disease and mild cognitive impairment in a Portuguese cohort.

  PMID 16824219 · PMC1534050 · BMC neurology · 2006 · 7 claims · 5 setups

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  The C282Y variant allele of HFE is significantly overrepresented in PD patients compared to controls, suggesting it confers higher risk for PD

  genomic same pooled pcr-rflp pcr-based cross-tabulation

• 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

• Resequencing PNMT in European hypertensive and normotensive individuals: no common susceptibilily variants for hypertension and purifying selection on intron 1.

  PMID 17645789 · PMC1947951 · BMC medical genetics · 2007 · 7 claims · 7 setups

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  Resequencing of PNMT found no common susceptibility variants that distinguish hypertensive from normotensive individuals

  genomic pnmt promoter pcr population haplotype

• Protective effect of paraoxonase 1 gene variant Gln192Arg in age-related macular degeneration.

  PMID 20042177 · PMC3026437 · American journal of ophthalmology · 2010 · 6 claims · 4 setups

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  The Gln192Arg PON1 polymorphism is associated with decreased susceptibility to AMD, particularly wet AMD, indicating a protective effect

  genomic pcr-amplified case-control pon1 single-strand direct genetic

• The (CTG)n polymorphism in the NOTCH4 gene is not associated with schizophrenia in Japanese individuals.

  PMID 11407996 · PMC32311 · BMC psychiatry · 2001 · 6 claims · 4 setups

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  No significant differences in genotype or allele frequencies of the NOTCH4 (CTG)n repeat were found between schizophrenia patients and controls

  genomic pcr genotype pcr-based direct pcr

• 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

• Association of Escherichia coli O157:H7 tir polymorphisms with human infection.

  PMID 17718910 · PMC2063500 · BMC infectious diseases · 2007 · 8 claims · 6 setups

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  tir polymorphisms 255 T>A and RR1-RU3 (presence/absence) associate strongly with human vs bovine isolate source

  stec pcr multiplex elisa

• PedGenie: an analysis approach for genetic association testing in extended pedigrees and genealogies of arbitrary size.

  PMID 16620382 · PMC1459209 · BMC bioinformatics · 2006 · 7 claims · 3 setups

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  PedGenie is a valid, flexible statistical tool for genetic association analysis in pedigrees of arbitrary size and structure using Monte Carlo significance testing

  simulated gaw12 breast monte pedigree-based genetic