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 44

System / cell line: normalized ✕ Assay: ratio ✕ Clear

Integrating genomic based information into clinical warfarin (Coumadin) management: an illustrative case report.

PMID 18763667 · PMC3696193 · Connecticut medicine · 2008 · 8 claims · 6 setups

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Combined CYP2C9 and VKORC1 genotype can explain up to 45% of warfarin dose variability

genomic edta plasma cardiac genotyping extraction inr
Late onset thrombosis in a case of severe protein S deficiency due to compound heterozygosity for PROS1 mutations.

PMID 18433462 · PMC2632602 · Journal of thrombosis and haemostasis : JTH · 2008 · 6 claims · 6 setups

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A novel 14 bp deletion in intervening sequence L (putative branch point of intron L), which likely impairs PROS1 pre-mRNA splicing, was found in all family members with low free protein S.

plasma genomic apc free ps-direct
Rapid detection of genomic imbalances using micro-arrays consisting of pooled BACs covering all human chromosome arms.

PMID 16221972 · PMC1253841 · Nucleic acids research · 2005 · 8 claims · 6 setups

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Reducing array complexity by pooling five BACs per spot (covering a chromosome arm) increases robustness to amplification-related ratio variation compared with single-BAC spotting

normal aneuploid same genomiphi-amplified array-cgh
Genome wide identification of recessive cancer genes by combinatorial mutation analysis.

PMID 18846217 · PMC2557123 · PloS one · 2008 · 7 claims · 4 setups

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A combinatorial mutation analysis identified 154 candidate recessive cancer genes (pRecessiveCancer<1.5x10-7, FDR=0.39)

refseq tp53 tumor 154-gene est paired array
Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis.

PMID 17363414 · PMC2779891 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2007 · 8 claims · 6 setups

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High-density oligonucleotide/SNP platforms are superior to the BAC platform for genome-wide detection of copy-number variations smaller than 1 Mb

genomic normalized simulated tiling-resolution snp oligonucleotide
Array-based profiling of reference-independent methylation status (aPRIMES) identifies frequent promoter methylation and consecutive downregulation of ZIC2 in pediatric medulloblastoma.

PMID 17344319 · PMC1874664 · Nucleic acids research · 2007 · 7 claims · 7 setups

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aPRIMES is a novel array-based method that detects direct (absolute) methylation status of CGIs via competitive hybridization of McrBC-digested (methylated) versus HpaII/BstUI-digested (unmethylated) DNA from the same genome, avoiding reference-tissue and copy-number biases

pediatric tumor eight desmoplastic aprimes bisulfite quantitative
Comprehensive comparison of gene expression diversity among a variety of human stem cells.

PMID 36458020 · PMC9706419 · NAR genomics and bioinformatics · 2022 · 6 claims · 7 setups

Has reproduction · 71

iPSC gene expression is more strongly influenced by tissue origin than other stem cell types, whereas ESCs and somatic stem cells (MSCs, HSCs) are more strongly impacted by culture condition.

undifferentiated stem batch-corrected bulk microarray batch
GAA repeat expansion mutation mouse models of Friedreich ataxia exhibit oxidative stress leading to progressive neuronal and cardiac pathology.

PMID 16919418 · PMC2842930 · Genomics · 2006 · 8 claims · 8 setups

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Human FXN YAC transgenes containing GAA repeat expansions (YG22, YG8) rescue the embryonic lethality of homozygous Fxn knockout mice

yg22 tissues lysates sciatic breeding semiquantitative western
MLGA--a rapid and cost-efficient assay for gene copy-number analysis.

PMID 17823203 · PMC2034490 · Nucleic acids research · 2007 · 8 claims · 4 setups

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MLGA is a novel selector-based technique using multiplex ligation-dependent circularization of genomic DNA fragments for copy-number analysis

pooled genomic aneuploid dog mlga
Magnetization transfer imaging in 'premanifest' Huntington's disease.

PMID 19823894 · PMC2837878 · Journal of neurology · 2010 · 8 claims · 4 setups

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MTI parameters (mean MTR and normalized peak height) of whole brain, grey matter and white matter did not differ significantly between premanifest HD carriers and non-carriers

premanifest magnetization 3d-t1-weighted clinical
Visualization of three-way comparisons of omics data.

PMID 17335588 · PMC1831488 · BMC bioinformatics · 2007 · 7 claims · 3 setups

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A novel HSB (hue, saturation, brightness) color-coding scheme can represent three-way comparisons of corresponding datapoints from three datasets.

liver replicate ce-tofms one-way electropherogram
Examination of FMR1 transcript and protein levels among 74 premutation carriers.

PMID 19927162 · PMC4122982 · Journal of human genetics · 2010 · 7 claims · 4 setups

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FMR1 premutation carriers (55-199 CGG repeats) show increased FMR1 transcript levels alongside decreased FMRP levels compared to normal individuals.

peripheral subset real-time western cgg
Search for genomic alterations in monozygotic twins discordant for cleft lip and/or palate.

PMID 19803774 · PMC2893889 · Twin research and human genetics : the official journal of the International Society for Twin Studies · 2009 · 7 claims · 5 setups

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Postzygotic genomic alterations are not a common cause of monozygotic twin discordance for isolated cleft lip and/or palate.

peripheral array custom snp
Exploiting convergent phenotypes to derive a pan-cancer cisplatin response gene expression signature.

PMID 37076665 · PMC10115855 · NPJ precision oncology · 2023 · 8 claims · 8 setups

Has reproduction · 50

A convergent-phenotype-based seed gene/co-expression method can extract consensus gene expression signatures predictive of response to chemotherapeutic drugs in the GDSC database

epithelial-based tcga gdsc muscle-invasive differential co-expression signature
SW-ARRAY: a dynamic programming solution for the identification of copy-number changes in genomic DNA using array comparative genome hybridization data.

PMID 15961730 · PMC1151590 · Nucleic acids research · 2005 · 7 claims · 5 setups

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SW-ARRAY, an adaptation of the Smith-Waterman dynamic programming algorithm, provides a sensitive and robust method for identifying copy-number changes in array CGH data

chromosome 16p array probe-by-probe sw-array
Sequence, "subtle" alternative splicing and expression of the CYYR1 (cysteine/tyrosine-rich 1) mRNA in human neuroendocrine tumors.

PMID 17442112 · PMC1863428 · BMC cancer · 2007 · 7 claims · 5 setups

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CYYR1 mRNA undergoes a 'subtle' alternative splicing event generating two isoforms (CAG- and CAG+) differing by a single alanine codon at the exon3/exon4 junction

neuroendocrine tumors normal cyyr1 rt-pcr quantitative psti
Validating discovered Cis-acting regulatory genetic variants: application of an allele specific expression approach to HapMap populations.

PMID 19116668 · PMC2605564 · PloS one · 2008 · 7 claims · 6 setups

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ASE is more robust than total gene expression approaches to environmental variation and trans-acting genetic factors, giving a cleaner representation of cis-acting effects.

hapmap combined coriell ceu allele-specific linear one-sample
Surface-enhanced laser desorption/ionization time-of-flight proteomic profiling of breast carcinomas identifies clinicopathologically relevant groups of patients similar to previously defined clusters from cDNA expression.

PMID 18510725 · PMC2481497 · Breast cancer research : BCR · 2008 · 7 claims · 7 setups

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Unsupervised hierarchical clustering of 130 SELDI-TOF peaks yielded six peak clusters and five distinct groups of breast cancer patients.

lysates breast microarrays imac-preseparated seldi-tof pilot immunohistochemistry
Analysis of X chromosome inactivation in autism spectrum disorders.

PMID 18361425 · PMC4867005 · American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics · 2008 · 6 claims · 5 setups

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No significant excess of skewed XCI was found in mothers of children with ASD or in affected girls compared to controls

genomic multiplex mecp2 four chromosome non-parametric mutation
Tissue proteomics reveals differential and compartment-specific expression of the homologs transgelin and transgelin-2 in lung adenocarcinoma and its stroma.

PMID 19848416 · PMC2789179 · Journal of proteome research · 2009 · 6 claims · 6 setups

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Transgelin (TAGLN), transgelin-2 (TAGLN2), and cyclophilin A (PPIA) are overexpressed in lung adenocarcinoma tissue compared to matched normal lung

matched excised additional formalin-fixed 2-d lc-ms quantitative

Experiments

Integrating genomic based information into clinical warfarin (Coumadin) management: an illustrative case report.

Late onset thrombosis in a case of severe protein S deficiency due to compound heterozygosity for PROS1 mutations.

Rapid detection of genomic imbalances using micro-arrays consisting of pooled BACs covering all human chromosome arms.

Genome wide identification of recessive cancer genes by combinatorial mutation analysis.

Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis.

Array-based profiling of reference-independent methylation status (aPRIMES) identifies frequent promoter methylation and consecutive downregulation of ZIC2 in pediatric medulloblastoma.

Comprehensive comparison of gene expression diversity among a variety of human stem cells.

GAA repeat expansion mutation mouse models of Friedreich ataxia exhibit oxidative stress leading to progressive neuronal and cardiac pathology.

MLGA--a rapid and cost-efficient assay for gene copy-number analysis.

Magnetization transfer imaging in 'premanifest' Huntington's disease.

Visualization of three-way comparisons of omics data.

Examination of FMR1 transcript and protein levels among 74 premutation carriers.

Search for genomic alterations in monozygotic twins discordant for cleft lip and/or palate.

Exploiting convergent phenotypes to derive a pan-cancer cisplatin response gene expression signature.

SW-ARRAY: a dynamic programming solution for the identification of copy-number changes in genomic DNA using array comparative genome hybridization data.

Sequence, "subtle" alternative splicing and expression of the CYYR1 (cysteine/tyrosine-rich 1) mRNA in human neuroendocrine tumors.

Validating discovered Cis-acting regulatory genetic variants: application of an allele specific expression approach to HapMap populations.

Surface-enhanced laser desorption/ionization time-of-flight proteomic profiling of breast carcinomas identifies clinicopathologically relevant groups of patients similar to previously defined clusters from cDNA expression.

Analysis of X chromosome inactivation in autism spectrum disorders.

Tissue proteomics reveals differential and compartment-specific expression of the homologs transgelin and transgelin-2 in lung adenocarcinoma and its stroma.