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 41

System / cell line: identified ✕ Assay: coding ✕ Clear

Ethnically diverse causes of Walker-Warburg syndrome (WWS): FCMD mutations are a more common cause of WWS outside of the Middle East.

PMID 18752264 · PMC2577713 · Human mutation · 2008 · 8 claims · 4 setups

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40% (16/40) of WWS families in this diverse cohort received a molecular diagnosis with mutations in POMT1, POMT2, FKRP or FCMD

genomic pomt2 population genome-wide pcr multiplex
Identifying synonymous regulatory elements in vertebrate genomes.

PMID 15980499 · PMC1160227 · Nucleic acids research · 2005 · 7 claims · 4 setups

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SynoR is a tool that performs de novo genome-wide identification of synonymous regulatory elements (SREs) using evolutionarily conserved TFBS modules as seeds

genome genes genome-wide gene tissue-specificity
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
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
Mutation analysis of the MSMB gene in familial prostate cancer.

PMID 19997100 · PMC2816656 · British journal of cancer · 2010 · 8 claims · 5 setups

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No deleterious mutations were found in the MSMB coding region in 192 familial prostate cancer cases

germline blood 161-nt genotype sanger taqman transcription
Mutations in NYX of individuals with high myopia, but without night blindness.

PMID 17392683 · PMC2642916 · Molecular vision · 2007 · 7 claims · 5 setups

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Two novel NYX missense mutations (Cys48Trp and Arg191Gln) were found in unrelated males with high myopia but no night blindness.

unrelated individuals high model direct sequencing electroretinogram
PigGIS: Pig Genomic Informatics System.

PMID 17090590 · PMC1669765 · Nucleic acids research · 2007 · 7 claims · 7 setups

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PigGIS identified 15,700 pig consensus sequences covering 18.5 Mb of homologous human exons

million pig matched wgs blastx repeat sequence
Retinitis pigmentosa: mutation analysis of RHO, PRPF31, RP1, and IMPDH1 genes in patients from India.

PMID 18552984 · PMC2426732 · Molecular vision · 2008 · 8 claims · 4 setups

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Coding/flanking regions of RHO, PRPF31, and IMPDH1, plus exons 4F/4G/4H of RP1, were PCR-amplified and directly sequenced in 48 isolated and 53 adRP Indian patients and 75 controls

genomic peripheral probands identified pcr reverse clinical
Identification of four novel cytochrome P4501B1 mutations (p.I94X, p.H279D, p.Q340H, and p.K433K) in primary congenital glaucoma patients.

PMID 20057908 · PMC2802296 · Molecular vision · 2009 · 8 claims · 4 setups

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Mutations in CYP1B1 are a major cause of PCG in the studied patient cohort

genomic cyp1b1 pcg pcr missense clinical
International sequencing consortium.

PMID 15174459 · PMC1315987 · Environmental health perspectives · 2004 · 8 claims · 6 setups

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The p19 viral silencing-suppressor protein selectively recognizes short (21-22 nt) silencing siRNAs by measuring duplex length, using tryptophan residues (Trp39, Trp42) as molecular calipers that stack against the siRNA end base pairs.

cirv blood sampled rice x-ray site-directed mass
In silico discovery of gene-coding variants in murine quantitative trait loci using strain-specific genome sequence databases.

PMID 12537567 · PMC151180 · Genome biology · 2002 · 6 claims · 4 setups

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Strain-specific mouse genome sequence databases can be used in a high-throughput in silico pipeline to discover gene-coding variants within murine QTLs, without de novo sequencing.

strains genomic celera blast-based targeted phred
Mutation analysis of the ATR gene in breast and ovarian cancer families.

PMID 15987455 · PMC1175065 · Breast cancer research : BCR · 2005 · 8 claims · 5 setups

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ATR mediates the DNA damage response by phosphorylating tumor suppressors such as p53, BRCA1 and CHK1, making it a plausible candidate breast/ovarian cancer susceptibility gene

index atr variant mutation direct variant
DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes.

PMID 15608249 · PMC539965 · Nucleic acids research · 2005 · 5 claims · 8 setups

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Comparative human-mouse genome analysis identifies conserved sequence tags (CSTs, >=70% identity over >=100bp) that frequently correspond to non-coding elements with putative regulatory or structural roles

identified cst csts comparative coding exon
Report of a Korean patient with cystic fibrosis, carrying Q98R and Q220X mutations in the CFTR gene.

PMID 16778407 · PMC2729969 · Journal of Korean medical science · 2006 · 7 claims · 8 setups

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The patient was diagnosed with cystic fibrosis based on elevated sweat chloride concentration and identification of two CFTR mutations.

korean forearm patient's lungs direct quantitative family
Retroposition and evolution of the DNA-binding motifs of YY1, YY2 and REX1.

PMID 17478514 · PMC1904287 · Nucleic acids research · 2007 · 8 claims · 5 setups

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62 YY1-related sequences were identified across genomes ranging from flying insects to humans, with high zinc finger domain conservation

genome insect yy1-related zinc blast sequence synonymous
Resequencing of genes for transforming growth factor beta1 (TGFB1) type 1 and 2 receptors (TGFBR1, TGFBR2), and association analysis of variants with diabetic nephropathy.

PMID 17319955 · PMC1808054 · BMC medical genetics · 2007 · 7 claims · 7 setups

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TGFβ1 is a crucial mediator in the pathogenesis of diabetic nephropathy, promoting renal hypertrophy and extracellular matrix accumulation.

genomic healthy irish case mutation direct taqman
High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi.

PMID 18660809 · PMC2652037 · Nature genetics · 2008 · 7 claims · 8 setups

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Evolution in the Typhi population is characterized by ongoing loss of gene function (pseudogene accumulation) rather than gain of function or diversifying selection.

salmonella sequenced typhi whole-genome snp-based selection
Mutations in the TOPORS gene cause 1% of autosomal dominant retinitis pigmentosa.

PMID 18509552 · PMC2391085 · Molecular vision · 2008 · 7 claims · 7 setups

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Point mutations and small insertions/deletions in TOPORS cause approximately 1% of adRP

genomic unrelated additional patients fluorescent multiplex sequencing
Report of the 9th HLPP Workshop October 2007, Seoul, Korea.

PMID 18683817 · PMC4601560 · Proteomics · 2008 · 8 claims · 8 setups

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An integrated separating-identifying platform identified 6788 proteins (≥2 peptides, 95% confidence) in Chinese human liver samples, including 3721 new to liver and 977 hypothetical proteins

chinese liver hbv-related mammalian shotgun transcriptome yeast
The genome of the ant Tetramorium bicarinatum reveals a tandem organization of venom peptides genes allowing the prediction of their regulatory and evolutionary profiles.

PMID 38245722 · PMC10800049 · BMC genomics · 2024 · 8 claims · 8 setups

Has reproduction · 100

44 venom peptide genes were identified, distributed across four of the eleven chromosomes and organized in tandem repeat clusters.

tetramorium bicarinatum vpg venom whole-genome blast gene

Experiments

Ethnically diverse causes of Walker-Warburg syndrome (WWS): FCMD mutations are a more common cause of WWS outside of the Middle East.

Identifying synonymous regulatory elements in vertebrate genomes.

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

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

Mutation analysis of the MSMB gene in familial prostate cancer.

Mutations in NYX of individuals with high myopia, but without night blindness.

PigGIS: Pig Genomic Informatics System.

Retinitis pigmentosa: mutation analysis of RHO, PRPF31, RP1, and IMPDH1 genes in patients from India.

Identification of four novel cytochrome P4501B1 mutations (p.I94X, p.H279D, p.Q340H, and p.K433K) in primary congenital glaucoma patients.

International sequencing consortium.

In silico discovery of gene-coding variants in murine quantitative trait loci using strain-specific genome sequence databases.

Mutation analysis of the ATR gene in breast and ovarian cancer families.

DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes.

Report of a Korean patient with cystic fibrosis, carrying Q98R and Q220X mutations in the CFTR gene.

Retroposition and evolution of the DNA-binding motifs of YY1, YY2 and REX1.

Resequencing of genes for transforming growth factor beta1 (TGFB1) type 1 and 2 receptors (TGFBR1, TGFBR2), and association analysis of variants with diabetic nephropathy.

High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi.

Mutations in the TOPORS gene cause 1% of autosomal dominant retinitis pigmentosa.

Report of the 9th HLPP Workshop October 2007, Seoul, Korea.

The genome of the ant Tetramorium bicarinatum reveals a tandem organization of venom peptides genes allowing the prediction of their regulatory and evolutionary profiles.