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).

• Chipping away at 'stemness'.

  PMID 15287966 · PMC507869 · Genome biology · 2004 · 8 claims · 6 setups

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  Global gene-expression analyses across five independent studies identify known and new candidate regulators of human ES-cell growth, self-renewal, and pluripotency.

  microarray sage custom

• Gene expression levels assessed by oligonucleotide microarray analysis and quantitative real-time RT-PCR -- how well do they correlate?

  PMID 15854232 · PMC1142514 · BMC genomics · 2005 · 8 claims · 2 setups

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  Correlations between qRT-PCR and microarray data are generally strong, especially when identical transcripts are targeted by both methods (r = 0.89 for fold-change).

  pediatric same oligonucleotide quantitative

• SIGMA: a system for integrative genomic microarray analysis of cancer genomes.

  PMID 17192189 · PMC1764892 · BMC genomics · 2006 · 7 claims · 6 setups

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  SIGMA is a user-friendly, web-based Java application for visualization and integrative analysis of array CGH data across multiple platforms.

  cancer lung breast array medip segmentation

• Integrative analysis of RUNX1 downstream pathways and target genes.

  PMID 18671852 · PMC2529319 · BMC genomics · 2008 · 7 claims · 8 setups

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  Integrating gene expression profiles from three independent RUNX1 perturbation platforms (FPD-AML patient cell lines, RUNX1/CBFβ overexpression in HeLa cells, Runx1 knockout mouse embryos) identifies RUNX1-regulated genes and downstream pathways

  lymphoblastic hela runx1 aml cdna microarray affymetrix

• Are gene expression microarray analyses reliable? A review of studies of retinoic acid responsive genes.

  PMID 15626329 · PMC5171945 · Genomics, proteomics & bioinformatics · 2003 · 6 claims · 8 setups

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  Published microarray studies aiming to identify RA-responsive genes show substantial, often contradictory, differences in results across research groups.

  nb4 tf1 tracheobronchial moser affymetrix cdna microarray

• A simple and robust method for connecting small-molecule drugs using gene-expression signatures.

  PMID 18518950 · PMC2464610 · BMC bioinformatics · 2008 · 8 claims · 4 setups

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  A new method for building reference gene-expression profiles and scoring/testing connections improves on the original Connectivity Map by enabling statistical significance testing of connections.

  lines random gene-expression connectivity

• 6th annual meeting of the Complex Trait Consortium.

  PMID 17906895 · PMC2042027 · Mammalian genome : official journal of the International Mammalian Genome Society · 2007 · 8 claims · 7 setups

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  The NIEHS Perlegen/resequencing project has generated over 8.5 million SNPs from 15 inbred mouse strains but shows a high false-negative discovery rate, with an estimated 45 million SNPs actually present.

  inbred recombinant yeast gallstone genome affymetrix microarray