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 997

System / cell line: gene-expression ✕ Clear

Cardiovascular genetic medicine: genomic assessment of prognosis and diagnosis in patients with cardiomyopathy and heart failure.

PMID 20559924 · PMC4745893 · Journal of cardiovascular translational research · 2008 · 8 claims · 6 setups

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Molecular signature analysis (MSA) uses machine-learning/classification methods (e.g., PAM/nearest shrunken centroids) on gene expression patterns to classify samples by phenotype for diagnosis, prognosis, or therapy response.

myocardial endomyocardial peripheral pbmcs microarray allomap gene
Identification of the transcriptional response of human intestinal mucosa to Lactobacillus plantarum WCFS1 in vivo.

PMID 18681965 · PMC2519092 · BMC genomics · 2008 · 8 claims · 6 setups

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1-h and 6-h intraduodenal exposure of human small intestinal mucosa to L. plantarum WCFS1 induces differential expression of 669 and 424 gene reporters, respectively.

duodenal microarray combined whole-genome proteome real-time
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
A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus.

PMID 18631455 · PMC2727981 · Immunity · 2008 · 7 claims · 8 setups

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Transcriptional modules constructed from coordinately expressed genes across 8 diseases form stable, biologically coherent functional units

pbmc genes monocytes original microarray literature stimulation
Current and future directions in genomics of amyotrophic lateral sclerosis.

PMID 18625410 · PMC3524513 · Physical medicine and rehabilitation clinics of North America · 2008 · 8 claims · 8 setups

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Familial ALS (FALS, 5-10% of cases) follows Mendelian autosomal dominant inheritance, with 20% caused by SOD1 mutations and 80% by unknown mutations

american sals dutch irish genome laser expression
Seeded Bayesian Networks: constructing genetic networks from microarray data.

PMID 18601736 · PMC2474592 · BMC systems biology · 2008 · 8 claims · 4 setups

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Seeding Bayesian Network analysis with prior networks derived from literature and/or PPI data improves recovery of known gene-gene interactions compared to BN analysis without a seed

leukemia interactome pubmed-indexed computational microarray yeast literature
Functional annotation and identification of candidate disease genes by computational analysis of normal tissue gene expression data.

PMID 18560577 · PMC2409962 · PloS one · 2008 · 7 claims · 5 setups

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Ranked Coexpression Groups (RCG) built from k=6 nearest coexpressed genes, combined with a majority-rule functional characterization, integrate multiple datasets/coexpression measures to generate high-confidence functional annotation predictions

normal genome-wide same omim microarray sage computational
BRCA1 and BRCA2 missense variants of high and low clinical significance influence lymphoblastoid cell line post-irradiation gene expression.

PMID 18497862 · PMC2375115 · PLoS genetics · 2008 · 8 claims · 6 setups

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BRCA1 and BRCA2 pathogenic mutation carriers have similar post-irradiation LCL gene expression profiles to each other, more so than to BRCAX samples without an LCS variant

lymphoblastoid lcl gene microarray unsupervised t-test
Transcription network construction for large-scale microarray datasets using a high-performance computing approach.

PMID 18366618 · PMC2386070 · BMC genomics · 2008 · 8 claims · 7 setups

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RMT removes the random noise component of the gene expression correlation matrix by testing its eigenvalue statistics against a null hypothesis derived from a truly random correlation matrix

yeast liver eight-node microarray k-means hybrid
Transcriptomics and adaptive genomics of the asymptomatic bacteriuria Escherichia coli strain 83972.

PMID 18317809 · PMC2329726 · Molecular genetics and genomics : MGG · 2008 · 8 claims · 7 setups

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Strain 83972 is best described as a 'deconstructed pathogen' rather than a true commensal that acquired fitness properties

coli microarrays microarray comparative processing
A non-parametric meta-analysis approach for combining independent microarray datasets: application using two microarray datasets pertaining to chronic allograft nephropathy.

PMID 18302764 · PMC2276496 · BMC genomics · 2008 · 8 claims · 6 setups

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A novel non-parametric meta-analysis approach for combining independent microarray datasets is presented, requiring no distributional assumptions and being logically intuitive.

kidney same identified additional microarray significance fisher's
In silico discovery of transcription regulatory elements in Plasmodium falciparum.

PMID 18257930 · PMC2268928 · BMC genomics · 2008 · 7 claims · 8 setups

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GEMS, using hypergeometric scoring and PWM parameter optimization, reliably identifies high-confidence cis-regulatory elements in the AT-rich, repeat-rich P. falciparum genome

falciparum plasmodium invasion invasion-related microarray motif comparative
Identification of gene interactions associated with disease from gene expression data using synergy networks.

PMID 18234101 · PMC2258206 · BMC systems biology · 2008 · 8 claims · 4 setups

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Synergy of a gene pair with respect to disease, defined as I(G1,G2;C) - [I(G1;C)+I(G2;C)], identifies gene pairs that interact cooperatively with respect to a phenotype rather than independently.

prostate simulated microarray simulated permutation
A taxonomy of epithelial human cancer and their metastases.

PMID 20017941 · PMC2806369 · BMC medical genomics · 2009 · 8 claims · 6 setups

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Unsupervised hierarchical clustering of 1566 primary epithelial tumors yields large tissue-enriched clusters (breast, colon/GI, lung, ovary, kidney) plus smaller prostate, thyroid-kidney, and mixed clusters

epithelial tumor metastatic breast microarray gene fisher
Filling gaps in PPAR-alpha signaling through comparative nutrigenomics analysis.

PMID 20003344 · PMC2801700 · BMC genomics · 2009 · 7 claims · 8 setups

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Meta-analysis of 16 microarray datasets across human, mouse, rat and yeast identifies 164 genes (MDEGs) consistently differentially expressed in response to high fat diet or PPAR signaling perturbation.

liver saccharomyces mdeg independent microarray transcription chromosomal
Cross species genomic analysis identifies a mouse model as undifferentiated pleomorphic sarcoma/malignant fibrous histiocytoma.

PMID 19956606 · PMC2779485 · PloS one · 2009 · 8 claims · 7 setups

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A 100-gene signature from LSL-KrasG12D;Trp53Flox/Flox mouse sarcomas (vs normal muscle) is specifically and significantly enriched in human MFH but not other soft tissue sarcoma subtypes across three independent human datasets.

lsl-krasg12d soft combined mfh microarray gene oncogenic
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
A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

PMID 19923232 · PMC2817484 · Nucleic acids research · 2010 · 8 claims · 7 setups

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A Perl-based pipeline that BLASTs/BLATs Illumina probe sequences against genomes and transcript databases (RefSeq, UCSC Known Genes, UniGene/GenBank, Ensembl) can classify probes by quality grade (Perfect/Good/Bad/No match) and is applicable across 8 BeadArray platforms and other array types

maqc hepatocytes japanese illeum microarray dasl sequence
Increasing the number of thyroid lesions classes in microarray analysis improves the relevance of diagnostic markers.

PMID 19893615 · PMC2764086 · PloS one · 2009 · 8 claims · 8 setups

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Simultaneous analysis of 347 thyroid samples across 12 histological classes from six datasets improves definition of diagnostic markers compared to prior binary-class studies

thyroid microarray gene real-time
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

Experiments

Cardiovascular genetic medicine: genomic assessment of prognosis and diagnosis in patients with cardiomyopathy and heart failure.

Identification of the transcriptional response of human intestinal mucosa to Lactobacillus plantarum WCFS1 in vivo.

Integrative analysis of RUNX1 downstream pathways and target genes.

A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus.

Current and future directions in genomics of amyotrophic lateral sclerosis.

Seeded Bayesian Networks: constructing genetic networks from microarray data.

Functional annotation and identification of candidate disease genes by computational analysis of normal tissue gene expression data.

BRCA1 and BRCA2 missense variants of high and low clinical significance influence lymphoblastoid cell line post-irradiation gene expression.

Transcription network construction for large-scale microarray datasets using a high-performance computing approach.

Transcriptomics and adaptive genomics of the asymptomatic bacteriuria Escherichia coli strain 83972.

A non-parametric meta-analysis approach for combining independent microarray datasets: application using two microarray datasets pertaining to chronic allograft nephropathy.

In silico discovery of transcription regulatory elements in Plasmodium falciparum.

Identification of gene interactions associated with disease from gene expression data using synergy networks.

A taxonomy of epithelial human cancer and their metastases.

Filling gaps in PPAR-alpha signaling through comparative nutrigenomics analysis.

Cross species genomic analysis identifies a mouse model as undifferentiated pleomorphic sarcoma/malignant fibrous histiocytoma.

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

A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

Increasing the number of thyroid lesions classes in microarray analysis improves the relevance of diagnostic markers.

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