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 60

System / cell line: database ✕ Assay: literature ✕ Clear

Systems biology of SNPs.

PMID 16820779 · PMC1681509 · Molecular systems biology · 2006 · 8 claims · 2 setups

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Co-sets are groups of enzymatic reactions that are perfectly correlated (correlation coefficient of 1) in a reconstructed metabolic network and represent functional modules.

mitochondrial genome-scale database
Large-scale and high-confidence proteomic analysis of human seminal plasma.

PMID 16709260 · PMC1779515 · Genome biology · 2006 · 8 claims · 6 setups

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923 proteins were identified with high confidence in seminal plasma from a single individual, combining results from three ejaculate samples

seminal same list combined sds-page database decoy
Phosphorylation states of cell cycle and DNA repair proteins can be altered by the nsSNPs.

PMID 16111488 · PMC1208866 · BMC cancer · 2005 · 8 claims · 4 setups

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15 of 89 nsSNPs (16.9%) studied were predicted to abolish or create phosphorylation sites in 14 of 32 proteins (44.0%)

orthologues repair case-control phosphorylation cross-species database
Towards precise classification of cancers based on robust gene functional expression profiles.

PMID 15774002 · PMC1274255 · BMC bioinformatics · 2005 · 6 claims · 7 setups

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Functional expression profiles (FEPs) achieve comparable or better classification performance than conventional gene expression profiles (GEPs) across four public microarray datasets

nci60 lymphoma fep go-annotated cdna recursive hypergeometric
Mutation spectrum of homogentisic acid oxidase (HGD) in alkaptonuria.

PMID 19862842 · PMC2830005 · Human mutation · 2009 · 8 claims · 6 setups

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Mutations in HGD, which encodes homogentisate dioxygenase, cause AKU by blocking conversion of homogentisic acid to maleylacetoacetic acid in the tyrosine catabolic pathway

aku hgd recombinant hgd missense splice
An integrated database of genes responsive to the Myc oncogenic transcription factor: identification of direct genomic targets.

PMID 14519204 · PMC328458 · Genome biology · 2003 · 8 claims · 6 setups

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The Myc Target Gene database integrates literature evidence to prioritize candidate Myc-responsive genes and cluster them into functional groups

p493 rodent types quantitative chromatin northern
AnimalQTLdb: a livestock QTL database tool set for positional QTL information mining and beyond.

PMID 17135205 · PMC1781224 · Nucleic acids research · 2007 · 7 claims · 3 setups

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AnimalQTLdb houses publicly available QTL data for multiple livestock species (pig, cattle, chicken) in one comparable database.

pig cattle blast comparative database
piRNABank: a web resource on classified and clustered Piwi-interacting RNAs.

PMID 17881367 · PMC2238943 · Nucleic acids research · 2008 · 6 claims · 4 setups

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piRNABank is a web-accessible database storing empirically known piRNA sequences and annotations for human, mouse and rat.

pirna mapped sequence genome sliding-window
A systematic comparative and structural analysis of protein phosphorylation sites based on the mtcPTM database.

PMID 17521420 · PMC1929158 · Genome biology · 2007 · 7 claims · 6 setups

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mtcPTM is a hierarchically organized database of human and mouse phosphosites that preserves experimental context, enabling comparison of phosphorylation patterns across conditions

nonredundant database high-throughput homology
An analysis of human microRNA and disease associations.

PMID 18923704 · PMC2559869 · PloS one · 2008 · 8 claims · 8 setups

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MicroRNAs tend to show similar dysfunctional evidence (both up- or both down-regulated) for diseases within the same disease cluster, and different dysfunctional evidence between different disease clusters.

literature-derived diseases mirnas mirna literature bipartite mirna
Haplotype frequencies at the DRD2 locus in populations of the East European Plain.

PMID 19793394 · PMC2765450 · BMC genetics · 2009 · 8 claims · 4 setups

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The three-locus TaqI B-TaqI D-TaqI A haplotype at DRD2 constitutes a powerful genetic marker reflecting the most ancient dispersal of anatomically modern humans

genomic genotype rflp haplotype pcr-rflp hardy-weinberg pairwise
SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions.

PMID 19934256 · PMC2808967 · Nucleic acids research · 2010 · 8 claims · 6 setups

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SuperCYP is a comprehensive relational database aggregating CYP enzyme, drug metabolism, SNP/mutation, and structural information from literature and web resources.

scientific pubmed cyp-drug cyp text mutation manual
Biased exon/intron distribution of cryptic and de novo 3' splice sites.

PMID 16141195 · PMC1197134 · Nucleic acids research · 2005 · 7 claims · 5 setups

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Cryptic 3'ss (from 3'YAG consensus mutations) are significantly more frequent in exons than in introns

disease authentic hek293t nuclear literature shapiro-senapathy splicing
QTL MatchMaker: a multi-species quantitative trait loci (QTL) database and query system for annotation of genes and QTL.

PMID 16381937 · PMC1347390 · Nucleic acids research · 2006 · 8 claims · 5 setups

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QTL MatchMaker integrates QTL information with physical, genetic and cytogenetic maps across human, mouse and rat genomes

pubmed ucsc laser-captured literature genome comparative
Gene Prospector: an evidence gateway for evaluating potential susceptibility genes and interacting risk factors for human diseases.

PMID 19063745 · PMC2613935 · BMC bioinformatics · 2008 · 8 claims · 5 setups

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Gene Prospector is a Web-based application that selects and prioritizes potential disease-related genes using a curated, updated literature database of genetic association studies

huge pdgene snps3d dbsnp curated comparative snp
Epidemiology of doublet/multiplet mutations in lung cancers: evidence that a subset arises by chronocoordinate events.

PMID 19005564 · PMC2579325 · PloS one · 2008 · 8 claims · 7 setups

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Doublet mutations are significantly more frequent in EGFR (6.0%) and TP53 (2.3%) in human lung cancer than spontaneous doublets in mouse lacI (0.7%), about 8-fold and 3-fold higher respectively.

egfr tp53 laci lung literature comparative statistical
Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks.

PMID 18782832 · PMC2686584 · Nucleic acids research · 2009 · 8 claims · 5 setups

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CTD is a manually curated knowledgebase that integrates chemical-gene interactions, chemical-disease relationships, and gene-disease relationships into a chemical-gene-disease triad

pubmed ctd manual computational case-study
A comprehensive literature review of haplotyping software and methods for use with unrelated individuals.

PMID 15814067 · PMC3525117 · Human genomics · 2005 · 7 claims · 2 setups

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Forty-six haplotyping programs were identified and reviewed, split into 43 designed for individual genotype data and three designed for pooled DNA samples.

pubmed identified literature software
Current status of use of high throughput nucleotide sequencing in rheumatology.

PMID 33408124 · PMC7789458 · RMD open · 2021 · 8 claims · 4 setups

Has reproduction · 83

RNA-Seq is the most represented HTS assay in rheumatology research (n=457, 65%), used for biomarker identification in blood or synovial tissue

pubmed sequence icd-11 sle semiautomated sequencing disease-name
Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

PMID 17576681 · PMC1934990 · Nucleic acids research · 2007 · 8 claims · 4 setups

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Cryptic 5'ss are best predicted by computational algorithms that accommodate nucleotide dependencies (e.g., Markov model, maximum entropy, maximum dependence decomposition) rather than by weight-matrix models

disease mammalian compiled literature minigene computational

Experiments

Systems biology of SNPs.

Large-scale and high-confidence proteomic analysis of human seminal plasma.

Phosphorylation states of cell cycle and DNA repair proteins can be altered by the nsSNPs.

Towards precise classification of cancers based on robust gene functional expression profiles.

Mutation spectrum of homogentisic acid oxidase (HGD) in alkaptonuria.

An integrated database of genes responsive to the Myc oncogenic transcription factor: identification of direct genomic targets.

AnimalQTLdb: a livestock QTL database tool set for positional QTL information mining and beyond.

piRNABank: a web resource on classified and clustered Piwi-interacting RNAs.

A systematic comparative and structural analysis of protein phosphorylation sites based on the mtcPTM database.

An analysis of human microRNA and disease associations.

Haplotype frequencies at the DRD2 locus in populations of the East European Plain.

SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions.

Biased exon/intron distribution of cryptic and de novo 3' splice sites.

QTL MatchMaker: a multi-species quantitative trait loci (QTL) database and query system for annotation of genes and QTL.

Gene Prospector: an evidence gateway for evaluating potential susceptibility genes and interacting risk factors for human diseases.

Epidemiology of doublet/multiplet mutations in lung cancers: evidence that a subset arises by chronocoordinate events.

Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks.

A comprehensive literature review of haplotyping software and methods for use with unrelated individuals.

Current status of use of high throughput nucleotide sequencing in rheumatology.

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.