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).

• 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

• OncoDB.HCC: an integrated oncogenomic database of hepatocellular carcinoma revealed aberrant cancer target genes and loci.

  PMID 17098932 · PMC1669730 · Nucleic acids research · 2007 · 7 claims · 6 setups

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  OncoDB.HCC integrates human HCC LOH, CGH, microarray/proteomic expression, PubMed-reported gene data, and rodent HCC QTLs into a single physical-map-based database

  paired hcc rodent semi-quantitative microarray comparative

• Insights into the physiology of childbirth using transcriptomics.

  PMID 16752954 · PMC1475648 · PLoS medicine · 2006 · 7 claims · 4 setups

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  Labor results in a change in the transcriptome in each component of the uterus studied

  uterine lower microarray quantitative re-analysis

• Genomic and proteomic profiling II: comparative assessment of gene expression profiles in leiomyomas, keloids, and surgically-induced scars.

  PMID 17718906 · PMC2039739 · Reproductive biology and endocrinology : RB&E · 2007 · 7 claims · 4 setups

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  1124 transcripts (1103 genes; 732 over-expressed, 371 under-expressed) are differentially expressed in leiomyomas compared to keloids/incisional scars

  keloid leiomyoma microarray quantitative

• Fibroblasts from patients with Diamond-Blackfan anaemia show abnormal expression of genes involved in protein synthesis, amino acid metabolism and cancer.

  PMID 19765279 · PMC2760583 · BMC genomics · 2009 · 8 claims · 5 setups

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  Global microarray profiling reveals 421 genes differentially expressed in DBA patient fibroblasts compared to healthy controls

  dermal same fibroblasts analysis microarray quantitative rt-pcr

• Genetics and functional genomics of type 2 diabetes mellitus.

  PMID 14659011 · PMC329413 · Genome biology · 2003 · 7 claims · 5 setups

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  Genome-wide transcription profiling of diabetic skeletal muscle reveals coordinated downregulation of oxidative phosphorylation genes, converging on PGC1α as a central regulator.

  skeletal population microarray real-time genetic

• Response rate of fibrosarcoma cells to cytotoxic drugs on the expression level correlates to the therapeutic response rate of fibrosarcomas and is mediated by regulation of apoptotic pathways.

  PMID 16001973 · PMC1183194 · BMC cancer · 2005 · 6 claims · 5 setups

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  The number of significantly differentially expressed probesets induced by each drug correlates with the known clinical therapeutic response rate of that drug in fibrosarcoma

  ht1080 ht1080-derived oligonucleotide quantitative gene

• Identification of miRNA targets with stable isotope labeling by amino acids in cell culture.

  PMID 16945957 · PMC1636363 · Nucleic acids research · 2006 · 8 claims · 4 setups

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  SILAC can be used for miRNA target identification

  hela 3'-utr silac microarray dual-luciferase

• Transcriptome and proteome expressions involved in insulin resistance in muscle and activated T-lymphocytes of patients with type 2 diabetes.

  PMID 18267303 · PMC5054231 · Genomics, proteomics & bioinformatics · 2007 · 8 claims · 8 setups

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  Gene expression of INSR, VDR, IDE, Akt, IRS-1, IRS-2, GLUT4, and glycolytic pathway enzymes is decreased at least 50% in T2DM muscle and activated T-cells versus non-diabetic controls

  activated skeletal muscle altered affymetrix quantitative sirna

• Systems biology and the host response to viral infection.

  PMID 18066032 · PMC7097743 · Nature biotechnology · 2007 · 8 claims · 8 setups

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  Systems biology integration of 'omics data (transcriptomics, proteomics, genomics) with computational modeling is needed to fully understand virus-host interactions and identify novel antiviral targets

  lung cd4 rhesus kshv microarray quantitative genomic

• Characterization of heterotypic interaction effects in vitro to deconvolute global gene expression profiles in cancer.

  PMID 17868458 · PMC2375029 · Genome biology · 2007 · 8 claims · 8 setups

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  Co-culture of certain breast cancer cell lines with stromal fibroblasts induces interferon-response genes (IRGs) in a subset of cancer cells

  mda-mb231 epithelial breast early-stage cdna quantitative facs

• Genomics of signaling crosstalk of estrogen receptor alpha in breast cancer cells.

  PMID 18365014 · PMC2268000 · PloS one · 2008 · 7 claims · 6 setups

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  Estrogen, growth factors and cAMP elicit surprisingly distinct ERα-dependent transcriptional responses in MCF7 cells

  mcf7 promoter cdna quantitative computational

• Gene-Expression Profiling Suggests Impaired Signaling via the Interferon Pathway in Cstb-/- Microglia.

  PMID 27355630 · PMC4927094 · PloS one · 2016 · 8 claims · 8 setups

  Has reproduction · 54

  In Cstb-/- microglia, 184 genes were differentially expressed relative to control, of which 33 were identified by both microarray and RNA-seq.

  analysis microarray rna-seq quantitative

• Application of functional genomics to the chimeric mouse model of HCV infection: optimization of microarray protocols and genomics analysis.

  PMID 16725047 · PMC1482685 · Virology journal · 2006 · 6 claims · 4 setups

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  Mouse liver mRNA cross-hybridizes to corresponding human gene probes on the Agilent Human 22K oligonucleotide microarray

  liver genomic hcv-infected agilent two-color semi-quantitative real-time

• Effects of DNA-targeted ionizing radiation produced by 5-[125I]iodo-2'-deoxyuridine on global gene expression in primary human cells.

  PMID 17594496 · PMC1934370 · BMC genomics · 2007 · 8 claims · 7 setups

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  125I-IUdR-induced DNA damage alters expression of only a limited subset of genes in primary human cells

  ag09319 gm05388 nhfk whole-genome quantitative dna-associated

• Functional genomics in zebrafish permits rapid characterization of novel platelet membrane proteins.

  PMID 19109564 · PMC2680375 · Blood · 2009 · 8 claims · 6 setups

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  Zebrafish morpholino knockdown combined with a laser-induced arterial thrombosis assay is a fast, powerful method for initial functional screening of novel platelet genes.

  blood platelets platelet-rich platelet whole-genome quantitative flow

• Genomic profiling of microRNA and messenger RNA reveals deregulated microRNA expression in prostate cancer.

  PMID 18676839 · PMC2597340 · Cancer research · 2008 · 8 claims · 7 setups

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  MicroRNA processing components (Dicer, DGCR8) and microRNA host genes (MCM7, C9orf5) are significantly up-regulated in prostate tumors versus non-tumor tissue

  prostate subset lncap 22rv1 microrna quantitative western

• Genes implicated in multiple sclerosis pathogenesis from consilience of genotyping and expression profiles in relapse and remission.

  PMID 18366677 · PMC2324081 · BMC medical genetics · 2008 · 8 claims · 7 setups

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  Distinct sets of dysregulated genes are found in peripheral blood during the relapse phase versus the remission phase of RRMS

  peripheral blood pooled trio gene quantitative promoter

• Stable patterns of gene expression regulating carbohydrate metabolism determined by geographic ancestry.

  PMID 20016837 · PMC2790609 · PloS one · 2009 · 8 claims · 6 setups

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  151 'geo-ancestral genes' were identified that are both differentially expressed between AA and CAU subjects and contain SNPs distinguishing YRI (African) from CEU (European) HapMap populations

  leukocytes leukocyte-derived archived comparison whole-genome quantitative snp

• Functional features of gene expression profiles differentiating gastrointestinal stromal tumours according to KIT mutations and expression.

  PMID 19943934 · PMC2794290 · BMC cancer · 2009 · 8 claims · 5 setups

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  Hundreds of genes differentiate GISTs according to KIT versus PDGFRA mutation and expression status, despite no discriminative profile for clinical/pathological parameters.

  frozen genomic formalin-fixed differentially microarray sequencing quantitative