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 214

System / cell line: identified ✕ Clear

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
Novel SOX2 mutations and genotype-phenotype correlation in anophthalmia and microphthalmia.

PMID 19921648 · PMC2787970 · American journal of medical genetics. Part A · 2009 · 7 claims · 4 setups

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SOX2 coding-region mutations were identified in 10 of 51 (19.6%) unrelated individuals with anophthalmia/microphthalmia

blood parents sox2-mutation-positive pcr parental clinical
Urinary proteomic profiling for diagnostic bladder cancer biomarkers.

PMID 19811072 · PMC3422861 · Expert review of proteomics · 2009 · 8 claims · 8 setups

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Single protein biomarkers (e.g., NMP-22, BTA) suffer from high false-positive rates and none have replaced cystoscopy or cytology for bladder cancer detection.

urine page gel 2d-dige
Mouse-specific tandem IgY7-SuperMix immunoaffinity separations for improved LC-MS/MS coverage of the plasma proteome.

PMID 19722698 · PMC2783519 · Journal of proteome research · 2009 · 7 claims · 6 setups

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Tandem IgY7-SuperMix separation nearly doubles overall proteome coverage compared to IgY7 flow-through alone (523 vs 263 confidently identified proteins)

plasma identified lc-ms sds-page spike-in
Identification of Key Genes in Atherosclerosis by Combined DNA Methylation and miRNA Expression Analyses.

PMID 35949126 · PMC9682560 · Anatolian journal of cardiology · 2022 · 7 claims · 7 setups

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10 key genes (TCF7L2, CACNA1C, NRP1, GABBR2, FANCC, DCK, CCDC88C, TCF12, ABLIM1, PBX1) are regulated by both aberrant DNA methylation and miRNA activity in atherosclerosis

aorta cardiovascular peripheral blood methylation mirna expression
Sequence changes in predicted promoter elements of STK11/LKB1 are unlikely to contribute to Peutz-Jeghers syndrome.

PMID 15774015 · PMC1084245 · BMC genomics · 2005 · 6 claims · 4 setups

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Integrated phylogenetic foot printing and transcription factor binding site (TFBS) prediction identified a consensus putative STK11/LKB1 promoter region between nucleotides -1090 and -1472

genomic phylogenetic direct high
Cystic fibrosis in Korean children:a case report identified by a quantitative pilocarpine iontophoresis sweat test and genetic analysis.

PMID 15716623 · PMC2808565 · Journal of Korean medical science · 2005 · 8 claims · 8 setups

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CF should be suspected in Korean/Asian children with chronic respiratory symptoms despite its rarity in Asian populations

korean family bronchial quantitative sweat cftr
Proteomics studies reveal important information on small molecule therapeutics: a case study on plasma proteins.

PMID 18973825 · PMC7185545 · Drug discovery today · 2008 · 8 claims · 8 setups

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Abundant plasma proteins (albumin, IgG, transferrin) act as 'molecular sponges' that bind and transport low molecular weight proteins/peptides and drugs, extending their half-life by preventing rapid renal clearance.

blood schizophrenia sjl serum proteomic differential comparative
Mutation survey of known LCA genes and loci in the Saudi Arabian population.

PMID 18936139 · PMC2695987 · Investigative ophthalmology & visual science · 2009 · 7 claims · 4 setups

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Mutations in the 13 known LCA genes were identified in only 24% (9/37) of Saudi Arabian LCA families, far lower than the ~65% mutation detection rate reported in European populations

leukocyte affected kkesh-060 direct str homozygosity
Novel mutations in BBS5 highlight the importance of this gene in non-Caucasian Bardet-Biedl syndrome patients.

PMID 18203199 · PMC2578871 · American journal of medical genetics. Part A · 2008 · 6 claims · 8 setups

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Two novel homozygous missense mutations in BBS5 (p.Gly72Ser and p.Thr183Ala) were identified in non-Caucasian BBS patients (Somali and Sri Lankan)

genomic somali sri ethnically dhplc snp sanger
A simple and efficient algorithm for genome-wide homozygosity analysis in disease.

PMID 19756043 · PMC2758715 · Molecular systems biology · 2009 · 8 claims · 4 setups

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A genome-wide AH analysis (GAHA) algorithm can identify disease-associated loci by comparing frequencies of homozygous segments between cases and controls using a z-statistic proportion test

unrelated simulated selected genes genome-wide statistical logistic
Involvement of potential pathways in malignant transformation from oral leukoplakia to oral squamous cell carcinoma revealed by proteomic analysis.

PMID 19691830 · PMC2746235 · BMC genomics · 2009 · 7 claims · 6 setups

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85 proteins are differentially and consistently expressed (>2-fold change, P<0.05) between paired OLK and OSCC tissues, including 52 up-regulated and 33 down-regulated proteins

paired list differentially oscc 2-de gene interaction
Evaluating Distribution and Prognostic Value of New Tumor-Infiltrating Lymphocytes in HCC Based on a scRNA-Seq Study With CIBERSORTx.

PMID 33043022 · PMC7527443 · Frontiers in medicine · 2020 · 6 claims · 8 setups

Has reproduction · 78

CIBERSORTx can combine scRNA-seq-derived signature matrices with bulk RNA-seq data to estimate proportions of 11 TIL subsets in HCC tumor and normal tissue

tcga degs cd4-gzma prognostic scrna-seq cibersortx differential
Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database.

PMID 19723305 · PMC2753363 · BMC microbiology · 2009 · 8 claims · 5 setups

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Using the ATCC 33277-specific genome annotation improves proteome coverage (more proteins identified and more abundance ratios calculated) compared to the W83 annotation

gingivalis whole-cell comparative gene
Advancement of biomarker discovery and validation through the HUPO plasma proteome project.

PMID 15502245 · PMC3839274 · Disease markers · 2004 · 7 claims · 3 setups

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Standardization of specimen collection, handling, storage, and choice of serum vs. plasma/anticoagulant is essential for comparable proteomic biomarker discovery.

plasma ppp reference identification quantitative specimen
Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages.

PMID 16034026 · PMC1179734 · Nucleic acids research · 2005 · 8 claims · 6 setups

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L1 insertions are directly responsible for genomic deletions (L1IMDs) confirmed in both human and chimpanzee genomes

hg16 genomic individuals element computational pcr pcr-based
ARSACS in the Dutch population: a frequent cause of early-onset cerebellar ataxia.

PMID 18465152 · PMC2441586 · Neurogenetics · 2008 · 8 claims · 8 setups

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37% (16/43) of Dutch index patients with early-onset recessive cerebellar ataxia carry SACS mutations, indicating ARSACS is far more frequent than previously estimated

genomic identified sacs-mutation-positive alleles pcr clinical brain
Multidimensional proteomics analysis of amniotic fluid to provide insight into the mechanisms of idiopathic preterm birth.

PMID 18431506 · PMC2315798 · PloS one · 2008 · 7 claims · 7 setups

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A novel 5-peak SELDI proteomic signature (Q-profile) in the 10-12.5 kDa mass range identifies a subgroup of women at risk for preterm birth without intra-amniotic inflammation or bleeding.

amniotic excised spot differentially seldi-tof fluorescence robotic
Glucokinase gene mutations: structural and genotype-phenotype analyses in MODY children from South Italy.

PMID 18382660 · PMC2270336 · PloS one · 2008 · 8 claims · 6 setups

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16 of 30 patients with suspected MODY (53%) carry GCK mutations, confirming GCK MODY diagnosis

genomic gck fasting pediatric direct molecular biochemical
BHD mutations, clinical and molecular genetic investigations of Birt-Hogg-Dubé syndrome: a new series of 50 families and a review of published reports.

PMID 18234728 · PMC2564862 · Journal of medical genetics · 2008 · 8 claims · 7 setups

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BHD germline mutation detection rate was 88% (51/58 families) using direct DNA sequencing

peripheral blood-derived folliculin chest direct subcloning sequence

Experiments

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

Novel SOX2 mutations and genotype-phenotype correlation in anophthalmia and microphthalmia.

Urinary proteomic profiling for diagnostic bladder cancer biomarkers.

Mouse-specific tandem IgY7-SuperMix immunoaffinity separations for improved LC-MS/MS coverage of the plasma proteome.

Identification of Key Genes in Atherosclerosis by Combined DNA Methylation and miRNA Expression Analyses.

Sequence changes in predicted promoter elements of STK11/LKB1 are unlikely to contribute to Peutz-Jeghers syndrome.

Cystic fibrosis in Korean children:a case report identified by a quantitative pilocarpine iontophoresis sweat test and genetic analysis.

Proteomics studies reveal important information on small molecule therapeutics: a case study on plasma proteins.

Mutation survey of known LCA genes and loci in the Saudi Arabian population.

Novel mutations in BBS5 highlight the importance of this gene in non-Caucasian Bardet-Biedl syndrome patients.

A simple and efficient algorithm for genome-wide homozygosity analysis in disease.

Involvement of potential pathways in malignant transformation from oral leukoplakia to oral squamous cell carcinoma revealed by proteomic analysis.

Evaluating Distribution and Prognostic Value of New Tumor-Infiltrating Lymphocytes in HCC Based on a scRNA-Seq Study With CIBERSORTx.

Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database.

Advancement of biomarker discovery and validation through the HUPO plasma proteome project.

Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages.

ARSACS in the Dutch population: a frequent cause of early-onset cerebellar ataxia.

Multidimensional proteomics analysis of amniotic fluid to provide insight into the mechanisms of idiopathic preterm birth.

Glucokinase gene mutations: structural and genotype-phenotype analyses in MODY children from South Italy.

BHD mutations, clinical and molecular genetic investigations of Birt-Hogg-Dubé syndrome: a new series of 50 families and a review of published reports.