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 525

Assay: functional ✕ Clear

Starvation-induced transgenerational inheritance of small RNAs in C. elegans.

PMID 25018105 · PMC4377509 · Cell · 2014 · 8 claims · 7 setups

Has reproduction · 64

L1 starvation induces changes in endogenous 22G small RNAs (STGs) that are inherited for at least three generations in fed descendants.

elegans small small sequencing lifespan
Comparing protein abundance and mRNA expression levels on a genomic scale.

PMID 12952525 · PMC193646 · Genome biology · 2003 · 8 claims · 8 setups

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Correlations between mRNA expression and protein abundance are generally poor or limited across most studies reviewed, including in yeast and human cancers

yeast laser-dissected serum myeloid two-dimensional seldi-tof isotope-coded
Polymorphism in the tumour necrosis factor receptor II gene is associated with circulating levels of soluble tumour necrosis factor receptors in rheumatoid arthritis.

PMID 16277675 · PMC1297570 · Arthritis research & therapy · 2005 · 8 claims · 6 setups

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The TNF-RII T676G polymorphism is associated with circulating levels of sTNF-RI and sTNF-RII in RA, with a trend TT > TG > GG

serum genomic peripheral synovial elisa pcr-rflp clinical
Inferring combinatorial regulation of transcription in silico.

PMID 15647509 · PMC546154 · Nucleic acids research · 2005 · 8 claims · 5 setups

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Combining Cluster-Buster (TFBS cluster prediction) with GOSSIP (rigorous GO enrichment statistics with multiple-testing/FDR correction) predicts biological functions controlled by combinatorial transcription factor action, without prior knowledge of factor targets

upstream monocytes same tfbs microarray permutation
Three novel and the common Arg677Ter RP1 protein truncating mutations causing autosomal dominant retinitis pigmentosa in a Spanish population.

PMID 16597330 · PMC1456953 · BMC medical genetics · 2006 · 8 claims · 5 setups

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Three novel RP1 truncating mutations (Gln686Ter, Lys705fsX712, Lys722fsX737) cause adRP

genomic adrp denaturing direct restriction
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
Multiple whole genome alignments and novel biomedical applications at the VISTA portal.

PMID 17488840 · PMC1933192 · Nucleic acids research · 2007 · 8 claims · 4 setups

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A novel multiple whole-genome alignment algorithm treats all genomes symmetrically, avoiding dependence on a single base/reference genome

genome vertebrate multi-species whole-genome conservation non-synonymous
A distinct epigenetic signature at targets of a leukemia protein.

PMID 17266773 · PMC1796549 · BMC genomics · 2007 · 7 claims · 7 setups

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Combining gene expression microarray analysis with bioinformatic search for AML1-consensus sequences identifies direct AML1 targets that expression analysis alone cannot resolve

32d sequence gene bioinformatic real-time
Genomic and proteomic profiling of oxidative stress response in human diploid fibroblasts.

PMID 18654835 · PMC4973579 · Biogerontology · 2009 · 8 claims · 7 setups

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Treatment of HCA3 human diploid fibroblasts with a mild dose of H2O2 (600 μM) induces premature senescence without killing the cells.

hca3 differentially mudpit cdna semi-quantitative
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
Investigation of the human tear film proteome using multiple proteomic approaches.

PMID 18334958 · PMC2268847 · Molecular vision · 2008 · 8 claims · 6 setups

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Tear collection method (capillary vs. Schirmer strip) significantly impacts which proteins are detected in the tear film proteome.

tear spectra 1d-sds-page 2d-sds-page mudpit
A novel mutation in FRMD7 causing X-linked idiopathic congenital nystagmus in a large family.

PMID 18246032 · PMC2267738 · Molecular vision · 2008 · 8 claims · 6 setups

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A novel c.812G>T transversion in exon 9 of FRMD7, causing p.C271F, is the causative mutation for XLICN in this family

affected family blood frmd7 microsatellite direct denaturing
The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice.

PMID 20368178 · PMC2894525 · Science translational medicine · 2009 · 7 claims · 6 setups

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Germ-free C57BL/6J mice can be stably and heritably colonized with a human fecal microbiota, reproducing much of the donor's bacterial diversity.

fecal postnatal luminal pooled 16s shotgun body
Mutations in the formin gene INF2 cause focal segmental glomerulosclerosis.

PMID 20023659 · PMC2980844 · Nature genetics · 2010 · 8 claims · 8 setups

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Mutations in INF2, a formin family actin-regulating protein, cause autosomal dominant focal segmental glomerulosclerosis (FSGS)

families genes individuals kidney genome-wide sanger resequencing
Meta-analysis of inter-species liver co-expression networks elucidates traits associated with common human diseases.

PMID 20019805 · PMC2787626 · PLoS computational biology · 2009 · 8 claims · 8 setups

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A novel semi-parametric meta-analysis method (based on a gene-centric Glass's d effect size) outperforms existing parametric and non-parametric meta-analysis methods at identifying functionally coherent gene pairs across species.

liver simulated conserved nearly gene simulation kolmogorov-smirnov
Proteomics identifies multipotent and low oncogenic risk stem cells of the spleen.

PMID 20005973 · PMC2891339 · The international journal of biochemistry & cell biology · 2010 · 8 claims · 5 setups

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CD45- splenic stem cell-specific proteins are identical to core iPS/ES markers OCT3/4, SOX2, KLF4, c-MYC and NANOG.

spleen cd45 hox11+ lc-ms rt-pcr immunofluorescence
Multi-organ expression profiling uncovers a gene module in coronary artery disease involving transendothelial migration of leukocytes and LIM domain binding 2: the Stockholm Atherosclerosis Gene Expression (STAGE) study.

PMID 19997623 · PMC2780352 · PLoS genetics · 2009 · 8 claims · 6 setups

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Functionally associated gene modules, not individual genes, underlie CAD development and can be identified via multi-organ expression clustering

liver atherosclerotic 128-gene independent two-way gene bioinformatic
Analysis of recent segmental duplications in the bovine genome.

PMID 19951423 · PMC2796684 · BMC genomics · 2009 · 8 claims · 6 setups

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Recently duplicated sequence (≥1 kb, ≥90% identity) comprises 3.11% (94.4 Mb) of the bovine genome assembly (Btau_4.0)

bos bovine genes cattle genome fluorescent repeat
Requirements for Pseudomonas aeruginosa acute burn and chronic surgical wound infection.

PMID 25057820 · PMC4109851 · PLoS genetics · 2014 · 8 claims · 8 setups

Has reproduction · 78

In vivo gene expression is generally not correlated with a gene's importance for fitness, with the exception of metabolic genes, for which differential expression is more predictive of fitness.

aeruginosa differentially paired rna-seq tn-seq computational
Cancer genomics identifies regulatory gene networks associated with the transition from dysplasia to advanced lung adenocarcinomas induced by c-Raf-1.

PMID 19812696 · PMC2754338 · PloS one · 2009 · 8 claims · 5 setups

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Comparison of tumor, transgenic, and non-transgenic lung cells reveals distinct and overlapping regulatory gene networks associated with progression to adenocarcinoma.

lung gene differentially significantly laser histology principal

Experiments

Starvation-induced transgenerational inheritance of small RNAs in C. elegans.

Comparing protein abundance and mRNA expression levels on a genomic scale.

Polymorphism in the tumour necrosis factor receptor II gene is associated with circulating levels of soluble tumour necrosis factor receptors in rheumatoid arthritis.

Inferring combinatorial regulation of transcription in silico.

Three novel and the common Arg677Ter RP1 protein truncating mutations causing autosomal dominant retinitis pigmentosa in a Spanish population.

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

Multiple whole genome alignments and novel biomedical applications at the VISTA portal.

A distinct epigenetic signature at targets of a leukemia protein.

Genomic and proteomic profiling of oxidative stress response in human diploid fibroblasts.

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

Investigation of the human tear film proteome using multiple proteomic approaches.

A novel mutation in FRMD7 causing X-linked idiopathic congenital nystagmus in a large family.

The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice.

Mutations in the formin gene INF2 cause focal segmental glomerulosclerosis.

Meta-analysis of inter-species liver co-expression networks elucidates traits associated with common human diseases.

Proteomics identifies multipotent and low oncogenic risk stem cells of the spleen.

Multi-organ expression profiling uncovers a gene module in coronary artery disease involving transendothelial migration of leukocytes and LIM domain binding 2: the Stockholm Atherosclerosis Gene Expression (STAGE) study.

Analysis of recent segmental duplications in the bovine genome.

Requirements for Pseudomonas aeruginosa acute burn and chronic surgical wound infection.

Cancer genomics identifies regulatory gene networks associated with the transition from dysplasia to advanced lung adenocarcinomas induced by c-Raf-1.