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 586

System / cell line: normal ✕ Clear

Gene-environment interaction and obesity.

PMID 19019037 · PMC3683966 · Nutrition reviews · 2008 · 8 claims · 8 setups

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Obesity susceptibility is largely genetically determined but requires environmental exposure (excess energy intake, low fiber, physical inactivity) to manifest phenotypically.

framingham european individuals healthy genome-wide candidate gene-diet
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
Brain-specific proteins decline in the cerebrospinal fluid of humans with Huntington disease.

PMID 18984577 · PMC2649809 · Molecular & cellular proteomics : MCP · 2009 · 8 claims · 6 setups

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Brain-specific proteins are 1.8 times more likely to be observed in CSF than in plasma

csf brain normal 2d-dige label-free isotopic
Proteomics of the lysosome.

PMID 18977398 · PMC2684028 · Biochimica et biophysica acta · 2009 · 8 claims · 8 setups

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The mammalian lysosome has been shown to contain ~60 soluble luminal proteins and ~25 transmembrane proteins

liver placenta brain conditioned lc-ms n-terminal man6-p
Phenotypic screening, transcriptional profiling, and comparative genomic analysis of an invasive and non-invasive strain of Candida albicans.

PMID 18950481 · PMC2579918 · BMC microbiology · 2008 · 8 claims · 8 setups

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Strain SC5314 is invasive and virulent whereas strain ATCC10231 is non-invasive and strongly attenuated in virulence

albicans hep-2 rhe blood phenotypic growth adhesion
Accuracy of predicting the genetic risk of disease using a genome-wide approach.

PMID 18852893 · PMC2561058 · PloS one · 2008 · 8 claims · 4 setups

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Deterministic equations can predict the accuracy (r_gĝ) of genome-wide genetic risk/value prediction for continuous, dichotomous, and case-control study designs.

simulated stochastic
Identification of two late acyltransferase genes responsible for lipid A biosynthesis in Moraxella catarrhalis.

PMID 18795947 · PMC2585779 · The FEBS journal · 2008 · 8 claims · 8 setups

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Two late acyltransferase genes, lpxX and lpxL, were identified in M. catarrhalis O35E by informatics analysis of the partial genome sequence

lipid proteinase catarrhalis suspensions maldi-tof fatty sds-page
Genetic and epigenetic contributions to human nutrition and health: managing genome-diet interactions.

PMID 18755320 · PMC5421377 · Journal of the American Dietetic Association · 2008 · 8 claims · 7 setups

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Folate-mediated one-carbon metabolism is a conduit linking the cellular nutrient environment to genome regulation via nucleotide biosynthesis for DNA synthesis and SAM biosynthesis for genome methylation.

yellow premenopausal men humans dietary mthfr plasma
Design and analysis issues in genome-wide somatic mutation studies of cancer.

PMID 18692126 · PMC2820387 · Genomics · 2009 · 6 claims · 4 setups

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Two-stage (discovery + validation) sequencing designs efficiently allocate resources and can produce highly informative candidate driver gene lists even with relatively small sample sizes.

hypothetical panel colorectal germline simulation targeted genome-wide
Molecular analysis of CHX10 and MFRP in Chinese subjects with primary angle closure glaucoma and short axial length eyes.

PMID 18648522 · PMC2480479 · Molecular vision · 2008 · 8 claims · 4 setups

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A rare CHX10 missense variant (c.728G>A, Gly243Asp) was identified in one PACG patient and absent in 215 controls, and is a possible disease-causing variant

genomic same chx10 pacg pcr case-control cross-species
A prospective, cross-sectional survey study of the natural history of Niemann-Pick disease type B.

PMID 18625664 · PMC2692309 · Pediatrics · 2008 · 8 claims · 8 setups

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NPD type B involves multisystem disease including hepatosplenomegaly, interstitial lung disease, dyslipidemia, thrombocytopenia, and growth delay

leukocyte peripheral serum plasma gene enzyme chitotriosidase
Defining disease with laser precision: laser capture microdissection in gastroenterology.

PMID 18619446 · PMC3736118 · Gastroenterology · 2008 · 8 claims · 8 setups

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LCM allows isolation of pure cell populations from heterogeneous tissue without damaging DNA, RNA, or protein integrity.

esophagus gastric colorectal colonic maldi cdna profiling
CCL genes in multiple sclerosis and systemic lupus erythematosus.

PMID 18602166 · PMC5301077 · Journal of neuroimmunology · 2008 · 7 claims · 5 setups

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Previously suggested borderline CCL marker/haplotype associations with MS are rejected after Bonferroni correction for multiple testing

genomic patients 17q11.2-q12 buccal snp linkage hardy-weinberg
A mouse to human search for plasma proteome changes associated with pancreatic tumor development.

PMID 18547137 · PMC2504036 · PLoS medicine · 2008 · 7 claims · 8 setups

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GEM models combined with in-depth proteomic analysis provide a useful strategy to identify candidate cancer markers applicable to human disease with potential for early detection

plasma immunodepleted pancreatic shotgun two-dimensional immunodepletion
Estimation of relevant variables on high-dimensional biological patterns using iterated weighted kernel functions.

PMID 18509521 · PMC2396875 · PloS one · 2008 · 7 claims · 6 setups

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wKIERA combines a weighted-kernel discriminant (kernel perceptron) with an iterative stochastic probability estimation-of-distribution algorithm to estimate a relevance distribution over variables

serum colon glioblastoma synthetic seldi-tof gene computational
Convergence of mutation and epigenetic alterations identifies common genes in cancer that predict for poor prognosis.

PMID 18507500 · PMC2429944 · PLoS medicine · 2008 · 7 claims · 7 setups

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At least 36 of the 189 newly mutated CAN genes are targets of promoter CpG island hypermethylation, often in both colon and breast cancer cell lines

breast same selected hct116 expression methylation-specific rt-pcr
Large-scale mutagenesis in p19(ARF)- and p53-deficient mice identifies cancer genes and their collaborative networks.

PMID 18485879 · PMC2405818 · Cell · 2008 · 8 claims · 8 setups

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A large-scale retroviral insertional mutagenesis screen identified 10,806 insertion sites implicating over 300 loci in tumorigenesis

p53 tumor tumors computational retroviral linker-mediated flow
A comparative study of techniques for differential expression analysis on RNA-Seq data.

PMID 25119138 · PMC4132098 · PloS one · 2014 · 8 claims · 8 setups

Has reproduction · 58

edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives.

brain neurospheres lymphoblastoid simulation single-end paired-end rna-seq
Anticipation in familial lattice corneal dystrophy type I with R124C mutation in the TGFBI (BIGH3) gene.

PMID 18470323 · PMC2373796 · Molecular vision · 2008 · 7 claims · 4 setups

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The R124C mutation (C417T) in exon 4 of TGFBI cosegregates with lattice corneal dystrophy type I in this Chilean family

members same genomic clinical stereopsis sanger
ATBF1 and NQO1 as candidate targets for allelic loss at chromosome arm 16q in breast cancer: absence of somatic ATBF1 mutations and no role for the C609T NQO1 polymorphism.

PMID 18416817 · PMC2377272 · BMC cancer · 2008 · 8 claims · 7 setups

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Five genes (NQO1, ATBF1, DBNDD1, HSBP1, CGI-38) at 16q show significantly lower mRNA expression in breast tumors with LOH at 16q compared to tumors without LOH

ductal same sporadic paired cdna quantitative genotyping

Experiments

Gene-environment interaction and obesity.

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

Brain-specific proteins decline in the cerebrospinal fluid of humans with Huntington disease.

Proteomics of the lysosome.

Phenotypic screening, transcriptional profiling, and comparative genomic analysis of an invasive and non-invasive strain of Candida albicans.

Accuracy of predicting the genetic risk of disease using a genome-wide approach.

Identification of two late acyltransferase genes responsible for lipid A biosynthesis in Moraxella catarrhalis.

Genetic and epigenetic contributions to human nutrition and health: managing genome-diet interactions.

Design and analysis issues in genome-wide somatic mutation studies of cancer.

Molecular analysis of CHX10 and MFRP in Chinese subjects with primary angle closure glaucoma and short axial length eyes.

A prospective, cross-sectional survey study of the natural history of Niemann-Pick disease type B.

Defining disease with laser precision: laser capture microdissection in gastroenterology.

CCL genes in multiple sclerosis and systemic lupus erythematosus.

A mouse to human search for plasma proteome changes associated with pancreatic tumor development.

Estimation of relevant variables on high-dimensional biological patterns using iterated weighted kernel functions.

Convergence of mutation and epigenetic alterations identifies common genes in cancer that predict for poor prognosis.

Large-scale mutagenesis in p19(ARF)- and p53-deficient mice identifies cancer genes and their collaborative networks.

A comparative study of techniques for differential expression analysis on RNA-Seq data.

Anticipation in familial lattice corneal dystrophy type I with R124C mutation in the TGFBI (BIGH3) gene.

ATBF1 and NQO1 as candidate targets for allelic loss at chromosome arm 16q in breast cancer: absence of somatic ATBF1 mutations and no role for the C609T NQO1 polymorphism.