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 57

System / cell line: oligonucleotide ✕ Assay: expression ✕ Clear

Sources of variability and effect of experimental approach on expression profiling data interpretation.

PMID 11936955 · PMC65691 · BMC bioinformatics · 2002 · 8 claims · 7 setups

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Intra-patient tissue heterogeneity (different regions of the same biopsy) is often the greatest source of variability in expression profiling

skeletal muscle spleen myogenic affymetrix duplicate unsupervised
Toxicogenomics research consortium sails into uncharted waters.

PMID 12460811 · PMC1241122 · Environmental health perspectives · 2002 · 8 claims · 8 setups

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The NIEHS-funded $37 million Toxicogenomics Research Consortium (TRC) combines the NIEHS Microarray Center with five academic institutions (UNC, Duke, Fred Hutchinson/UW, MIT, OHSU) to define genetic variability, set gene expression standards, and study environmental stress responses.

strains nervous mice liver microarray gene toxicogenomic
Large-scale analysis of Macaca fascicularis transcripts and inference of genetic divergence between M. fascicularis and M. mulatta.

PMID 18294402 · PMC2287170 · BMC genomics · 2008 · 8 claims · 6 setups

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Constructed full-length-enriched cDNA libraries and determined 85,721 EST sequences and 9407 full-insert sequences from cynomolgus macaque brain (7 regions), testis, and liver

cynomolgus 3-year-old macaque est full-insert oligonucleotide
Canine tumor cross-species genomics uncovers targets linked to osteosarcoma progression.

PMID 20028558 · PMC2803201 · BMC genomics · 2009 · 8 claims · 7 setups

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High expression of IL-8 and SLC1A3, identified via cross-species mining, is associated with poor outcome in an independent population of human osteosarcoma patients

canine osteosarcoma independent third oligonucleotide cross-species quantitative
Using DNA microarrays to study host-microbe interactions.

PMID 10998383 · PMC2627958 · Emerging infectious diseases · 2000 · 8 claims · 8 setups

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DNA microarrays can measure transcript levels and detect sequence polymorphisms for every gene simultaneously in microbial genomes

streptococcus cytomegalovirus coli mycobacterium oligonucleotide microarray gene
Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues.

PMID 16188928 · PMC4631381 · Bioinformatics (Oxford, England) · 2005 · 7 claims · 4 setups

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Genes upregulated in squamous cell lung cancer are highly connected (well-connected) nodes in the protein interactome

squamous ophid degs oligonucleotide interaction connectivity
Genomic characterisation of a Fgf-regulated gradient-based neocortical protomap.

PMID 16079153 · PMC4729368 · Development (Cambridge, England) · 2005 · 7 claims · 7 setups

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Neocortical progenitor cells show rostrocaudal gradients of gene expression rather than discrete domains/compartments

neocortex dorsal cortex embryo oligonucleotide microarray non-isotopic
Application of functional genomics to primate endometrium: insights into biological processes.

PMID 17118168 · PMC1775064 · Reproductive biology and endocrinology : RB&E · 2006 · 8 claims · 7 setups

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Gene expression profiles differ distinctly across proliferative, early-, mid-, and late-secretory phases of the human menstrual cycle, reflecting sequential estradiol and progesterone action.

endometrial uterus whole-genome cdna oligonucleotide
'Genome design' model and multicellular complexity: golden middle.

PMID 17062620 · PMC1635334 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Intermediately expressed human genes are the longest genes genome-wide, in both coding and intronic sequence, longer than housekeeping or tissue-specific genes.

normal genes proteins encoded oligonucleotide gene functional
Organismal complexity, cell differentiation and gene expression: human over mouse.

PMID 17881362 · PMC2095826 · Nucleic acids research · 2007 · 8 claims · 7 setups

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Human shows a greater fraction of tissue-specific genes and a greater ratio of total expression of tissue-specific to housekeeping genes than mouse across 32 homologous tissues

human-mouse oligonucleotide exon comparative
Peripheral blood B lymphocytes derived from patients with idiopathic pulmonary arterial hypertension express a different RNA pattern compared with healthy controls: a cross sectional study.

PMID 18269757 · PMC2262076 · Respiratory research · 2008 · 7 claims · 4 setups

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IPAH patients' peripheral blood B-lymphocytes express a distinct RNA profile compared with healthy controls

peripheral pbmc oligonucleotide flow density
Sex genes for genomic analysis in human brain: internal controls for comparison of probe level data extraction.

PMID 12962547 · PMC212256 · BMC bioinformatics · 2003 · 8 claims · 3 setups

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RMA-generated gene expression values are markedly less variable and more reliable than MAS5.0- and MBEI-derived values

postmortem oligonucleotide real-time quality
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
Overview of microarray analysis of gene expression and its applications to cervical cancer investigation.

PMID 18182341 · PMC7129792 · Taiwanese journal of obstetrics & gynecology · 2007 · 6 claims · 5 setups

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Oligonucleotide microarray and cDNA microarray are the two main microarray platforms used to study gene expression genome-wide.

cervical cdna microarray combinatorial
Leveraging two-way probe-level block design for identifying differential gene expression with high-density oligonucleotide arrays.

PMID 15099405 · PMC411067 · BMC bioinformatics · 2004 · 7 claims · 2 setups

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Two-way ANOVA and Mack-Skillings tests on probe-level data with FDR control are substantially more powerful than t-test/Wilcoxon on probe-set level data for detecting differential expression

fibroblast background high-density
Unravelling the hidden heterogeneities of diffuse large B-cell lymphoma based on coupled two-way clustering.

PMID 17888167 · PMC2082044 · BMC genomics · 2007 · 8 claims · 6 setups

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A proposed coupled two-way clustering (CTWC/SPC) method combined with a GO-based functional concept consistency score can identify compact, robust gene subsets that define clinically meaningful DLBCL subtypes

dlbcl identified microarray oligonucleotide coupled
Functional genomics of early cortex patterning.

PMID 16515721 · PMC1431711 · Genome biology · 2006 · 7 claims · 6 setups

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The neocortical protomap is established as continuous rostro-caudal gradients of gene expression in progenitor cells, not discrete compartments

neocortex embryonic fgfr1-mutant cortex oligonucleotide situ microarray
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
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
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

Sources of variability and effect of experimental approach on expression profiling data interpretation.

Toxicogenomics research consortium sails into uncharted waters.

Large-scale analysis of Macaca fascicularis transcripts and inference of genetic divergence between M. fascicularis and M. mulatta.

Canine tumor cross-species genomics uncovers targets linked to osteosarcoma progression.

Using DNA microarrays to study host-microbe interactions.

Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues.

Genomic characterisation of a Fgf-regulated gradient-based neocortical protomap.

Application of functional genomics to primate endometrium: insights into biological processes.

'Genome design' model and multicellular complexity: golden middle.

Organismal complexity, cell differentiation and gene expression: human over mouse.

Peripheral blood B lymphocytes derived from patients with idiopathic pulmonary arterial hypertension express a different RNA pattern compared with healthy controls: a cross sectional study.

Sex genes for genomic analysis in human brain: internal controls for comparison of probe level data extraction.

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

Overview of microarray analysis of gene expression and its applications to cervical cancer investigation.

Leveraging two-way probe-level block design for identifying differential gene expression with high-density oligonucleotide arrays.

Unravelling the hidden heterogeneities of diffuse large B-cell lymphoma based on coupled two-way clustering.

Functional genomics of early cortex patterning.

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

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

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.