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 561

System / cell line: exon ✕ Clear

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
Mutation analysis of genes that control the G1/S cell cycle in melanoma: TP53, CDKN1A, CDKN2A, and CDKN2B.

PMID 15819981 · PMC1097717 · BMC cancer · 2005 · 7 claims · 4 setups

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TP53 gene shows heterozygous defects in 8 of 39 (20.5%) melanoma tumors, including novel point mutations and novel SNPs in intronic sequences

metastatic melanoma genomic pcr-sscp sequencing pcr
Genomic organization, annotation, and ligand-receptor inferences of chicken chemokines and chemokine receptor genes based on comparative genomics.

PMID 15790398 · PMC1082905 · BMC genomics · 2005 · 8 claims · 6 setups

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Twenty-three chemokine genes and 14 chemokine receptor genes were identified in the chicken genome, including 12 new chemokines and 7 new receptors beyond prior reports.

chicken comparative amino phylogenetic
Two modes of microsatellite instability in human cancer: differential connection of defective DNA mismatch repair to dinucleotide repeat instability.

PMID 15778432 · PMC1067522 · Nucleic acids research · 2005 · 8 claims · 8 setups

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Dinucleotide microsatellite alterations in human cancer fall into two distinct modes: Type A (length changes ≤6 bp) and Type B (changes ≥8 bp)

msh2− mlh1− lymphomas colorectal fluorescent sequencing immunohistochemistry
Speeding disease gene discovery by sequence based candidate prioritization.

PMID 15766383 · PMC1274252 · BMC bioinformatics · 2005 · 7 claims · 8 setups

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Disease genes (OMIM) differ significantly from non-disease genes in sequence-based features including gene/cDNA/protein size, exon number, homolog conservation, secretion signal, 3' UTR length, CpG islands, and distance to nearest gene.

ensembl training same hgmd comparative machine tenfold
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
Low density DNA microarray for detection of most frequent TP53 missense point mutations.

PMID 15713227 · PMC553977 · BMC biotechnology · 2005 · 7 claims · 6 setups

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A double tandem hybridization microarray with 7-nt gap targets and 7-mer capture probes can search for 9 point mutations in TP53 codons 248, 249, and 273

genomic pcr six same pcr single-stranded oligonucleotide
Switching base preferences of mismatch cleavage in endonuclease V: an improved method for scanning point mutations.

PMID 17130153 · PMC1702505 · Nucleic acids research · 2007 · 8 claims · 4 setups

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A single Y80A alanine substitution switches Tma endo V from purine-preferring to essentially C-specific mismatch cleavage, including the previously refractory C/C mismatch.

synthetic k-ras endo pcr restriction
Recurring genomic breaks in independent lineages support genomic fragility.

PMID 17090315 · PMC1636669 · BMC evolutionary biology · 2006 · 6 claims · 6 setups

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The propensity of a chromosomal region to break is significantly correlated among independent lineages, even after accounting for covariates like region length and functional class.

hg17 genome computationally comparative marker segmental
Atypical haemolytic uraemic syndrome associated with a hybrid complement gene.

PMID 17076561 · PMC1626556 · PLoS medicine · 2006 · 6 claims · 7 setups

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Affected members of a previously genetically unsolved aHUS family carry a heterozygous CFH/CFHL1 hybrid gene (exons 1-21 from CFH, exons 22/23 from CFHL1)

peripheral genomic convalescent cdna genomic breakpoint-spanning
Expression of full-length p53 and its isoform Deltap53 in breast carcinomas in relation to mutation status and clinical parameters.

PMID 17054774 · PMC1636663 · Molecular cancer · 2006 · 7 claims · 7 setups

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The alternative splice isoform Δp53 mRNA is co-expressed with full-length p53 mRNA in breast tumors and cell lines

breast universal p53 subset qrt-pcr bioinformatic structure
Novel heteroduplex method using small cytology specimens with a remarkably high success rate for analysing EGFR gene mutations with a significant correlation to gefitinib efficacy in non-small-cell lung cancer.

PMID 17047654 · PMC2360725 · British journal of cancer · 2006 · 7 claims · 5 setups

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LH-MSA enables EGFR mutation analysis using small numbers of cancer cells from cytology specimens with a remarkably high success rate

cytology excised nsclc gefitinib-treated lh-mobility pcr clinical
A homozygous R262Q mutation in the gonadotropin-releasing hormone receptor presenting as constitutional delay of growth and puberty with subsequent borderline oligospermia.

PMID 16968799 · PMC1865483 · The Journal of clinical endocrinology and metabolism · 2006 · 7 claims · 8 setups

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A homozygous R262Q GNRHR mutation was identified in two brothers from an Asian Indian family, one of 11 families studied with delayed puberty or discordant IHH/delayed puberty siblings.

blood serum younger brothers mutational hormone 24-hour
Vertebrate gene finding from multiple-species alignments using a two-level strategy.

PMID 16925840 · PMC1810555 · Genome biology · 2006 · 8 claims · 5 setups

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DOGFISH cleanly separates a multi-species alignment classifier (RVM cascade) from an HMM-based structure predictor, avoiding tight coupling of alignment complexity with HMM formalism

genomic encode entire chromosome multi-species hmm-based classifier
GENCODE: producing a reference annotation for ENCODE.

PMID 16925838 · PMC1810553 · Genome biology · 2006 · 8 claims · 8 setups

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GENCODE annotation combines initial manual annotation by HAVANA, experimental validation, and refinement based on results to identify protein-coding genes in ENCODE regions

tissues encode rt-pcr comparative automated
AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome.

PMID 16925833 · PMC1810548 · Genome biology · 2006 · 8 claims · 5 setups

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AUGUSTUS predicted significantly more genes correctly than any other ab initio program in EGASP

genome human-mouse genes initio comparative extrinsic
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

Experiments

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

Mutation analysis of genes that control the G1/S cell cycle in melanoma: TP53, CDKN1A, CDKN2A, and CDKN2B.

Genomic organization, annotation, and ligand-receptor inferences of chicken chemokines and chemokine receptor genes based on comparative genomics.

Two modes of microsatellite instability in human cancer: differential connection of defective DNA mismatch repair to dinucleotide repeat instability.

Speeding disease gene discovery by sequence based candidate prioritization.

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

Low density DNA microarray for detection of most frequent TP53 missense point mutations.

Switching base preferences of mismatch cleavage in endonuclease V: an improved method for scanning point mutations.

Recurring genomic breaks in independent lineages support genomic fragility.

Atypical haemolytic uraemic syndrome associated with a hybrid complement gene.

Expression of full-length p53 and its isoform Deltap53 in breast carcinomas in relation to mutation status and clinical parameters.

Novel heteroduplex method using small cytology specimens with a remarkably high success rate for analysing EGFR gene mutations with a significant correlation to gefitinib efficacy in non-small-cell lung cancer.

A homozygous R262Q mutation in the gonadotropin-releasing hormone receptor presenting as constitutional delay of growth and puberty with subsequent borderline oligospermia.

Vertebrate gene finding from multiple-species alignments using a two-level strategy.

GENCODE: producing a reference annotation for ENCODE.

AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome.

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.