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 494

System / cell line: structure ✕ Clear

Mutations in TRPV4 cause Charcot-Marie-Tooth disease type 2C.

PMID 20037586 · PMC2812627 · Nature genetics · 2010 · 8 claims · 8 setups

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Heterozygous missense mutations in TRPV4 (c.805C>T/R269C and c.806G>A/R269H) cause CMT2C

cmt2c affected spinal drg genetic sanger quantitative
Mutational analysis of TARDBP in neurodegenerative diseases.

PMID 20031275 · PMC2889148 · Neurobiology of aging · 2011 · 8 claims · 4 setups

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TARDBP mutations are not a significant cause of AD or PD

als tdp-43 pcr pathogenicity
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
A small-cell lung cancer genome with complex signatures of tobacco exposure.

PMID 20016488 · PMC2880489 · Nature · 2010 · 8 claims · 7 setups

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22,910 somatic substitutions, including 132 in coding exons, were identified genome-wide in the NCI-H209 SCLC genome.

nci-h209 sclc lu-135 massively pcr multiplex
Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.

PMID 20003482 · PMC2807441 · BMC genomics · 2009 · 8 claims · 6 setups

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Manual annotation of the mouse Chromosome 8 defensin region identifies 98 gene loci: 54 in the alpha-defensin cluster and 44 in the beta-defensin cluster

c57bl orthologous alpha-defensin defensin manual comparative sequence
The other side of comparative genomics: genes with no orthologs between the cow and other mammalian species.

PMID 20003425 · PMC2808326 · BMC genomics · 2009 · 7 claims · 4 setups

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3,801 bovine genes have no orthologs in human, mouse and dog, and 1,010 human genes have no orthologs in cow despite having orthologs in mouse and dog

bovine cow coding blast-based ensembl gene
PCP consensus sequences of flaviviruses: correlating variance with vector competence and disease phenotype.

PMID 19969003 · PMC2822003 · Journal of molecular biology · 2010 · 7 claims · 7 setups

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PCP-consensus sequences of E protein show insertions/deletions that distinguish tick-borne, mosquito-borne, no-known-vector (NKV), and yellow fever virus (YFV) Flaviviruses

natural aligned ns3 denv sequence pcp-consensus physicochemical
A restricted spectrum of NRAS mutations causes Noonan syndrome.

PMID 19966803 · PMC3118669 · Nature genetics · 2010 · 8 claims · 6 setups

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Germline NRAS mutations (T50I, G60E) cause a subset of Noonan syndrome cases via enhanced MAPK activation

cohort cos-7 recombinant nras mutation western ras
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
Genome reannotation of Escherichia coli CFT073 with new insights into virulence.

PMID 19930606 · PMC2785843 · BMC genomics · 2009 · 8 claims · 7 setups

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Reannotation excluded 608 CDSs from the original RefSeq annotation, mostly unfunctional 'hypothetical'/'putative' genes

coli c0139r blastp rps-blast initio
Characterization of the influenza A H5N1 viruses of the 2008-09 outbreaks in India reveals a third introduction and possible endemicity.

PMID 19924254 · PMC2775943 · PloS one · 2009 · 7 claims · 5 setups

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All 2008-09 Indian H5N1 isolates belong to the EMA3 sublineage of clade 2.2

h5n1 gene genome phylogenetic bayesian
Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer.

PMID 19922616 · PMC2784454 · BMC biology · 2009 · 8 claims · 7 setups

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The ratio of homologous recombination to mutation in B. pseudomallei is over two times higher than in Streptococcus pneumoniae, the highest yet reported in bacteria.

isolates genome snp snps multilocus genome bayesian
MEROPS: the peptidase database.

PMID 19892822 · PMC2808883 · Nucleic acids research · 2010 · 8 claims · 5 setups

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MEROPS is a manually curated hierarchical classification of peptidases and protein inhibitors organized into protein species, families, and clans based on sequence and structural homology.

archaean holotype c-x-c proteins comparative domain substrate
Comparative analysis of plant genomes allows the definition of the "Phytolongins": a novel non-SNARE longin domain protein family.

PMID 19889231 · PMC2779197 · BMC genomics · 2009 · 8 claims · 6 setups

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A novel, plant-specific family of longin-related proteins, the 'Phytolongins', was identified in land plant genomes.

genomes longin plant phytolongin iterative phylogenetic genomic
Intrinsic structural disorder confers cellular viability on oncogenic fusion proteins.

PMID 19888473 · PMC2768585 · PLoS computational biology · 2009 · 8 claims · 5 setups

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Translocation-related human proteins are significantly enriched in intrinsic structural disorder compared to all human proteins

translocation-related translocation cyclin-dependent intrinsic pfam randomized
Identification and functional analyses of 11,769 full-length human cDNAs focused on alternative splicing.

PMID 19880432 · PMC2780955 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2009 · 8 claims · 5 setups

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Identified 23,241 human genes transcribed into protein-coding mRNAs using full-length cDNA and 5'-EST sequence data

tissues genome full-length genes full-length genome orf
Discovering the phylodynamics of RNA viruses.

PMID 19855824 · PMC2756585 · PLoS computational biology · 2009 · 8 claims · 8 setups

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A comprehensive 'discovery phase' integrating ecological and evolutionary dynamics of RNA viruses across scales is needed to achieve a full phylodynamic understanding

h3n2 influenza avian foot-and-mouth bayesian phylogenetic whole-genome
Mutation analysis in primary immunodeficiency diseases: case studies.

PMID 19841577 · PMC2774237 · Current opinion in allergy and clinical immunology · 2009 · 8 claims · 8 setups

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Genomic DNA Sanger sequencing is the standard first-line approach for identifying PIDD-causing mutations but has limitations that can yield false-negative or false-positive results

mother parents ebv-transformed nemo genomic flow northern
An intergenic non-coding rRNA correlated with expression of the rRNA and frequency of an rRNA single nucleotide polymorphism in lung cancer cells.

PMID 19838300 · PMC2759515 · PloS one · 2009 · 8 claims · 7 setups

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An nc-rRNA is transcribed from the intergenic spacer upstream of the rRNA transcription start site in human lung epithelial and lung cancer cells, spanning roughly -1000 to at least +203/+300.

lung hpl1d rrna external pcr rt-pcr quantitative
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

Mutations in TRPV4 cause Charcot-Marie-Tooth disease type 2C.

Mutational analysis of TARDBP in neurodegenerative diseases.

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

A small-cell lung cancer genome with complex signatures of tobacco exposure.

Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.

The other side of comparative genomics: genes with no orthologs between the cow and other mammalian species.

PCP consensus sequences of flaviviruses: correlating variance with vector competence and disease phenotype.

A restricted spectrum of NRAS mutations causes Noonan syndrome.

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

Genome reannotation of Escherichia coli CFT073 with new insights into virulence.

Characterization of the influenza A H5N1 viruses of the 2008-09 outbreaks in India reveals a third introduction and possible endemicity.

Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer.

MEROPS: the peptidase database.

Comparative analysis of plant genomes allows the definition of the "Phytolongins": a novel non-SNARE longin domain protein family.

Intrinsic structural disorder confers cellular viability on oncogenic fusion proteins.

Identification and functional analyses of 11,769 full-length human cDNAs focused on alternative splicing.

Discovering the phylodynamics of RNA viruses.

Mutation analysis in primary immunodeficiency diseases: case studies.

An intergenic non-coding rRNA correlated with expression of the rRNA and frequency of an rRNA single nucleotide polymorphism in lung cancer cells.

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