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 103

System / cell line: gene-expression ✕ Assay: quantitative ✕ Clear

BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources.

PMID 19919682 · PMC3091323 · Genome biology · 2009 · 8 claims · 4 setups

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BioGPS aggregates distributed, third-party gene annotation resources into a single customizable portal for human, mouse, and rat genes.

biogps diverse tissues specified web reference exon
Genetic and functional association of FAM5C with myocardial infarction.

PMID 18430236 · PMC2383879 · BMC medical genetics · 2008 · 8 claims · 5 setups

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SNPs within FAM5C show genetic linkage to and association with myocardial infarction in the GENECARD family-based sample

genecard cathgen donor aortic genome-wide case-control expression
Genome-wide association studies of MRI-defined brain infarcts: meta-analysis from the CHARGE Consortium.

PMID 20044523 · PMC2923092 · Stroke · 2010 · 8 claims · 6 setups

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SNP rs2208454 in intron 3 of MACROD2 (near FLRT3, chr20p12) is associated with lower risk of covert MRI-infarcts (OR=0.76, p=4.64x10-7)

stroke-free elderly african-american cardiovascular genome-wide direct expression
Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans.

PMID 18193044 · PMC2682493 · Nature genetics · 2008 · 8 claims · 7 setups

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GWAS plus targeted replication identified 18 loci reproducibly associated with LDL cholesterol, HDL cholesterol, and/or triglycerides, six of which are newly identified

blood liver fasting genome-wide targeted liver
The future is genome-wide.

PMID 16934105 · PMC1779592 · Genome biology · 2006 · 8 claims · 8 setups

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Noncoding SNPs near NRG1 associated with schizophrenia likely act by influencing NRG1 expression level

schizophrenia myocardial individuals infectious genetic candidate gene
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
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
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
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
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
Testing whether genetic variation explains correlation of quantitative measures of gene expression, and application to genetic network analysis.

PMID 18444230 · PMC2729096 · Statistics in medicine · 2008 · 8 claims · 3 setups

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A statistical test (delta method and Steiger-Browne optimal linear composites) is developed to test equality of the marginal correlation and the partial correlation of two gene expression traits conditional on a set of covariates.

simulated real analytical simulation application
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
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
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
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
Identification of novel gene amplifications in breast cancer and coexistence of gene amplification with an activating mutation of PIK3CA.

PMID 19706770 · PMC2745517 · Cancer research · 2009 · 8 claims · 8 setups

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Genome-wide DNA copy number analysis of 161 primary breast tumors identified six novel focally amplified genes: POLD3, IRAK4, IRX2, TBL1XR1, ASPH, and BRD4

breast mcf10a mcf10ca1h snp quantitative rt-qpcr
Expression analysis of secreted and cell surface genes of five transformed human cell lines and derivative xenograft tumors.

PMID 15836779 · PMC1112590 · BMC genomics · 2005 · 8 claims · 3 setups

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A custom 60-mer oligonucleotide microarray covering 3531 secreted and cell surface genes was designed to profile 5 transformed human cell lines and their derivative xenograft tumors.

carcinoma derivative xenograft custom quantitative
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

Experiments

BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources.

Genetic and functional association of FAM5C with myocardial infarction.

Genome-wide association studies of MRI-defined brain infarcts: meta-analysis from the CHARGE Consortium.

Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans.

The future is genome-wide.

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

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

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

Genetics and functional genomics of type 2 diabetes mellitus.

Insights into the physiology of childbirth using transcriptomics.

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

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

Testing whether genetic variation explains correlation of quantitative measures of gene expression, and application to genetic network analysis.

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

Systems biology and the host response to viral infection.

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

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

Identification of novel gene amplifications in breast cancer and coexistence of gene amplification with an activating mutation of PIK3CA.

Expression analysis of secreted and cell surface genes of five transformed human cell lines and derivative xenograft tumors.

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.