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 577

Assay: exon ✕ Clear

EGASP: Introduction.

PMID 16925831 · PMC1810546 · Genome biology · 2006 · 8 claims · 5 setups

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Computational gene finding methods, when compared to the GENCODE golden standard annotation, show that the human genome annotation is nearly complete in terms of novel protein-coding loci.

genome computational manual rt-pcr
Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs.

PMID 16914452 · PMC1557807 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Analysis of 56,419 full-length cDNAs identified 6877 alternative splicing genes encoding 18,297 alternative splicing variants made of 37,670 exons.

full-length deduced alternative panel cdna-to-genome manual motif
Transcriptome analysis reveals differential splicing events in IPF lung tissue.

PMID 24647608 · PMC3960165 · PloS one · 2014 · 8 claims · 6 setups

Has reproduction · 81

873 genes are differentially expressed in IPF lung tissue versus healthy controls at FDR<5%, with more up-regulated than down-regulated genes.

lung discovery gene gse24206 sequencing rna-seq real-time
Comparative genomic mapping of the bovine Fragile Histidine Triad (FHIT) tumour suppressor gene: characterization of a 2 Mb BAC contig covering the locus, complete annotation of the gene, analysis of cDNA and of physiological expression profiles.

PMID 16719907 · PMC1513570 · BMC genomics · 2006 · 8 claims · 5 setups

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A 2 Mb BAC contig of 78 clones was assembled covering the entire bovine FHIT locus

bovine pcr-based comparative rt-pcr
LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq.

PMID 24709818 · PMC4079972 · Genome research · 2014 · 8 claims · 8 setups

Has reproduction · 68

LaSSO (Lariat Sequence Site Origin) identifies intronic lariat reads and pinpoints branch points genome-wide from RNA-seq data by considering every intronic base as a potential branch point and including all possible exon-skipping lariats.

schizosaccharomyces pombe rna-seq lasso lariat-specific
Eight previously unidentified mutations found in the OA1 ocular albinism gene.

PMID 16646960 · PMC1468396 · BMC medical genetics · 2006 · 7 claims · 5 setups

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Sequencing of the nine OA1 exons in 72 individuals identified ten different mutations across seven unrelated families and three sporadic cases.

genomic oa1 direct long-range splice-site
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
PRKCA and multiple sclerosis: association in two independent populations.

PMID 16596167 · PMC1420678 · PLoS genetics · 2006 · 8 claims · 8 setups

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PRKCA (protein kinase C alpha) on 17q24 is associated with MS in Finnish families

finnish canadian unrelated blood snp dense multipoint
Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat.

PMID 16536879 · PMC1479377 · BMC bioinformatics · 2006 · 8 claims · 6 setups

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ENACE, a cross-species EST-to-genome comparison algorithm, can identify novel cassette-on exons and retained introns for EST-scanty species and distinguish conserved vs lineage-specific exons

presumably orthologous enace genes cross-species rt-pcr-sequencing nonsynonymous-to-synonymous
Microsatellite instability analysis in hereditary non-polyposis colon cancer using the Bethesda consensus panel of microsatellite markers in the absence of proband normal tissue.

PMID 16426447 · PMC1373649 · BMC medical genetics · 2006 · 7 claims · 4 setups

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MSI status can be determined in the absence of proband non-tumor tissue by comparing tumor alleles to alleles carried by the proband's progenitors

proband's peripheral hmsh2 microsatellite direct targeted
Peroxisomal proliferator activated receptor-gamma deficiency in a Canadian kindred with familial partial lipodystrophy type 3 (FPLD3).

PMID 16412238 · PMC1368963 · BMC medical genetics · 2006 · 8 claims · 6 setups

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A novel PPARG nonsense mutation, Y355X, was identified in a mother and daughter with FPLD3-consistent phenotypes and was absent from unaffected relatives and 260 healthy controls

subjects nih3t3 subject healthy sequencing luciferase western
The Proteomic Code: a molecular recognition code for proteins.

PMID 17999762 · PMC2206014 · Theoretical biology & medical modelling · 2007 · 8 claims · 8 setups

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The Proteomic Code is a set of rules by which genetic information is transferred into the physico-chemical properties of amino acids, determining protein-protein interactions and folding; it is part of the redundant Genetic Code.

anti-peptide sequence exon smooth radioimmunoassay pairwise genome-wide
High resolution melting for mutation scanning of TP53 exons 5-8.

PMID 17764544 · PMC2025602 · BMC cancer · 2007 · 7 claims · 5 setups

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HRM is an effective technique for rapid scanning of TP53 mutations that can markedly reduce required sequencing

tp53-mutant ovarian breast high hrm dideoxy
Sulfonylurea therapy in two Korean patients with insulin-treated neonatal diabetes due to heterozygous mutations of the KCNJ11 gene encoding Kir6.2.

PMID 17728498 · PMC2693808 · Journal of Korean medical science · 2007 · 7 claims · 4 setups

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Two Korean children with PND carry heterozygous KCNJ11 mutations (K170R and V59M) affecting Kir6.2.

peripheral case molecular continuous serum
Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility.

PMID 17554261 · PMC2628541 · Nature genetics · 2007 · 8 claims · 8 setups

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IRGM SNPs (rs13361189, rs4958847) show strong replicated association with Crohn disease; IRGM induces autophagy and control of intracellular bacteria

wtccc replication population cases genome-wide taqman snp
Three novel mutations in KIF21A highlight the importance of the third coiled-coil stalk domain in the etiology of CFEOM1.

PMID 17511870 · PMC1888713 · BMC genetics · 2007 · 8 claims · 5 setups

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Most individuals with CFEOM1 and rare individuals with CFEOM3 harbor heterozygous mutations in KIF21A

genomic pedigree proband pcr denaturing dhplc
Mutation screen and association studies in the diacylglycerol O-acyltransferase homolog 2 gene (DGAT2), a positional candidate gene for early onset obesity on chromosome 11q13.

PMID 17477860 · PMC1871603 · BMC genetics · 2007 · 7 claims · 5 setups

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DGAT2 is a plausible positional and functional candidate gene for obesity due to its localization at chr.11q13 (a linkage region) and its key role in triglyceride synthesis

extremely families genome sanger case-control family-based
Screening of the transcriptional regulatory regions of vascular endothelial growth factor receptor 2 (VEGFR2) in amyotrophic lateral sclerosis.

PMID 17456229 · PMC1868706 · BMC medical genetics · 2007 · 7 claims · 4 setups

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No mutations were identified in the VEGFR2 gene (exons 7, 18, 21, 27, promoter, or 5' UTR) in ALS patients

genomic pcr als direct restriction allele
Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

PMID 17452356 · PMC1904267 · Nucleic acids research · 2007 · 8 claims · 7 setups

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PASE (Prediction of Alternative Signaling Exons) is a computational algorithm combining Markov splice-site models, a Bayesian classifier, species conservation, and Scansite motif scoring to identify novel alternative cassette exons involved in cell signaling.

elegans pooled pcr known semi-nested cloning initio
Severe loss-of-function mutations in the adrenocorticotropin receptor (ACTHR, MC2R) can be found in patients diagnosed with salt-losing adrenal hypoplasia.

PMID 17223989 · PMC1859977 · Clinical endocrinology · 2007 · 7 claims · 5 setups

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MC2R mutations can be found in children diagnosed with salt-losing forms of adrenal hypoplasia

genomic plasma children direct plasma standard

Experiments

EGASP: Introduction.

Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs.

Transcriptome analysis reveals differential splicing events in IPF lung tissue.

Comparative genomic mapping of the bovine Fragile Histidine Triad (FHIT) tumour suppressor gene: characterization of a 2 Mb BAC contig covering the locus, complete annotation of the gene, analysis of cDNA and of physiological expression profiles.

LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq.

Eight previously unidentified mutations found in the OA1 ocular albinism gene.

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

PRKCA and multiple sclerosis: association in two independent populations.

Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat.

Microsatellite instability analysis in hereditary non-polyposis colon cancer using the Bethesda consensus panel of microsatellite markers in the absence of proband normal tissue.

Peroxisomal proliferator activated receptor-gamma deficiency in a Canadian kindred with familial partial lipodystrophy type 3 (FPLD3).

The Proteomic Code: a molecular recognition code for proteins.

High resolution melting for mutation scanning of TP53 exons 5-8.

Sulfonylurea therapy in two Korean patients with insulin-treated neonatal diabetes due to heterozygous mutations of the KCNJ11 gene encoding Kir6.2.

Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility.

Three novel mutations in KIF21A highlight the importance of the third coiled-coil stalk domain in the etiology of CFEOM1.

Mutation screen and association studies in the diacylglycerol O-acyltransferase homolog 2 gene (DGAT2), a positional candidate gene for early onset obesity on chromosome 11q13.

Screening of the transcriptional regulatory regions of vascular endothelial growth factor receptor 2 (VEGFR2) in amyotrophic lateral sclerosis.

Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

Severe loss-of-function mutations in the adrenocorticotropin receptor (ACTHR, MC2R) can be found in patients diagnosed with salt-losing adrenal hypoplasia.