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 353

System / cell line: analysis ✕ Assay: exon ✕ Clear

Expression and mutational analysis of c-kit in ovarian surface epithelial tumors.

PMID 16479070 · PMC2733984 · Journal of Korean medical science · 2006 · 8 claims · 3 setups

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KIT protein expression by immunohistochemistry is more frequent in mucinous ovarian tumors (borderline and malignant) than in serous tumors

ovarian genomic immunohistochemistry pcr-sscp
Molecular evolution of Cide family proteins: novel domain formation in early vertebrates and the subsequent divergence.

PMID 18500987 · PMC2426694 · BMC evolutionary biology · 2008 · 8 claims · 5 setups

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Sequences homologous to the CIDE-N domain/NCD show a wide phylogenetic distribution, from hydra and sea anemone to mammals, while true Cide proteins are restricted to vertebrates.

organisms cide cideb hmmer tblastn sequence
Molecular cloning, genomic characterization and over-expression of a novel gene, XRRA1, identified from human colorectal cancer cell HCT116Clone2_XRR and macaque testis.

PMID 12908878 · PMC194569 · BMC genomics · 2003 · 8 claims · 7 setups

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XRRA1 is a novel gene down-regulated ~2-fold in XR-resistant HCT116 Clone2_XRR relative to HCT116 Clone10, identified via cDNA microarray

hct116 macaque cos-7 genomic cdna est molecular
Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse.

PMID 18439302 · PMC2432081 · BMC genomics · 2008 · 8 claims · 7 setups

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Adjacent cassette exon pairs can be categorized by EST-derived correlation coefficient into three groups: mutually exclusive (ME, r<=-0.7), independent (IND, -0.2<=r<=0.2), and linked (LNK, r>=0.7)

human-mouse adjacent est genome splice
The androgen receptor CAG repeat polymorphism and modification of breast cancer risk in BRCA1 and BRCA2 mutation carriers.

PMID 15743497 · PMC1064126 · Breast cancer research : BCR · 2005 · 7 claims · 5 setups

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The AR CAG repeat polymorphism does not modify breast cancer risk in BRCA1 mutation carriers

peripheral brca1 same simulated fluorescent cox weighted
Segregation of a M404V mutation of the p62/sequestosome 1 (p62/SQSTM1) gene with polyostotic Paget's disease of bone in an Italian family.

PMID 16277682 · PMC1297578 · Arthritis research & therapy · 2005 · 6 claims · 4 setups

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The M404V mutation in p62/SQSTM1 exon 8 segregates with the polyostotic form of PDB in the F01 Italian family

genomic serum affected pcr pcr biochemical clinical
A genome-wide survey demonstrates widespread non-linear mRNA in expressed sequences from multiple species.

PMID 16237125 · PMC1258171 · Nucleic acids research · 2005 · 8 claims · 6 setups

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A genome-wide computational survey identifies 245 genes in mammals (264 across six species) that produce RREO events in expressed sequences

expressed representative random genes computational orf statistical
Improving melanoma classification by integrating genetic and morphologic features.

PMID 18532874 · PMC2408611 · PLoS medicine · 2008 · 7 claims · 5 setups

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BRAF-mutant melanomas show distinct morphological features (upward migration and nesting of intraepidermal melanocytes, epidermal thickening, sharper lateral demarcation, larger/rounder/more pigmented tumor cells) compared to non-mutant melanomas

archival same subset patients histopathological mutation quantitative
Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness.

PMID 19895688 · PMC3091318 · Genome biology · 2009 · 8 claims · 6 setups

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MacroRNA and lincRNA exons are subject to the same relatively low degree of sequence constraint, contrary to prior reports that lincRNAs are far more conserved

macrorna sequence comparative mouse-human population
Gene expression and isoform variation analysis using Affymetrix Exon Arrays.

PMID 18990248 · PMC2585104 · BMC genomics · 2008 · 8 claims · 7 setups

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The Exon Array performs comparably to 3'-targeted platforms (Illumina, U133) at the gene expression level, though interplatform correlation is slightly lower than between the two 3' platforms.

brain exon targeted principal
Ovarian cancer has frequent loss of heterozygosity at chromosome 12p12.3-13.1 (region of TEL and Kip1 loci) and chromosome 12q23-ter: evidence for two new tumour-suppressor genes.

PMID 9155043 · PMC2228239 · British journal of cancer · 1997 · 8 claims · 4 setups

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Two commonly deleted regions on chromosome 12 were identified in ovarian cancer: 12p12.3-13.1 (6/23 samples) and 12q23-ter (7/23 samples)

ovarian loh pcr-sscp multiplex
Molecular variants of the ATM gene in Hodgkin's disease in children.

PMID 14735203 · PMC2409549 · British journal of cancer · 2004 · 8 claims · 4 setups

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Missense variants of the ATM gene occur in childhood Hodgkin lymphoma but at low frequency (9%), and thus do not play a major role in oncogenesis of the disease

frozen matched paired rt-pcr germ-line sscp
Transcription of the human and rodent SPAM1 / PH-20 genes initiates within an ancient endogenous retrovirus.

PMID 15804358 · PMC1079825 · BMC genomics · 2005 · 8 claims · 8 setups

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Human, mouse, and rat SPAM1/Spam1 transcripts initiate within an ERV1 pol (internal coding) region rather than within an LTR

testis panel genome 5'-race non-quantitative
Analysis of copy number variation using quantitative interspecies competitive PCR.

PMID 18697816 · PMC2553599 · Nucleic acids research · 2008 · 7 claims · 6 setups

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qicPCR uses the entire genome of a single chimpanzee as a competitor, requiring only one reference sample for all assays and enabling large-scale multiplexing

genomic single 22q11ds qicpcr-derived qicpcr mlpa fluorescence
Multiple epiphyseal dysplasia.

PMID 19995321 · PMC2823319 · Acta orthopaedica · 2009 · 8 claims · 4 setups

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An exon 3/intron 3 donor splice mutation (IVS3DS [+2] T>C) in COL9A2 was identified in all affected family members

family patients microsatellite sequencing clinical
Large-scale trends in the evolution of gene structures within 11 animal genomes.

PMID 16518452 · PMC1386723 · PLoS computational biology · 2006 · 8 claims · 5 setups

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Change in intron–exon gene structure is gradual, clock-like, and largely independent of coding-sequence (protein) evolution

annotated animal unannotated comparative all-against-all neighbor-joining
Alternative splicing and bioinformatic analysis of human U12-type introns.

PMID 17332017 · PMC1874599 · Nucleic acids research · 2007 · 8 claims · 6 setups

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The long, evolutionarily conserved polypyrimidine (Py) tract of the JNK2 U2-U12 hybrid intron provides the signal for default inclusion of the downstream alternative exon 6b in non-neuronal cells

hela hek293 genome jnk2 rt-pcr minigene bioinformatic
Core signaling pathways in human pancreatic cancers revealed by global genomic analyses.

PMID 18772397 · PMC2848990 · Science (New York, N.Y.) · 2008 · 8 claims · 6 setups

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Pancreatic cancers contain an average of 63 genetic alterations, the majority of which are point mutations

pancreatic computational targeted prevalence snp
Divergence of exonic splicing elements after gene duplication and the impact on gene structures.

PMID 19883501 · PMC3091315 · Genome biology · 2009 · 8 claims · 7 setups

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ESEs and ESSs diverge especially fast shortly after gene duplication, correlating with time since duplication (Ks)

paralogous human-mouse duplicated comparative ortholog binomial
Screening of the Fc epsilon RI-beta-gene in a Swiss population of asthmatic children: no association with E237G and identification of new sequence variations.

PMID 10427478 · PMC3851081 · Disease markers · 1998 · 8 claims · 6 setups

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E237G shows no significant association with atopy or asthma in the Swiss population (3.7% in patients vs 2.6% in controls)

genomic extracted cdna patients pcr rt-pcr restriction

Experiments

Expression and mutational analysis of c-kit in ovarian surface epithelial tumors.

Molecular evolution of Cide family proteins: novel domain formation in early vertebrates and the subsequent divergence.

Molecular cloning, genomic characterization and over-expression of a novel gene, XRRA1, identified from human colorectal cancer cell HCT116Clone2_XRR and macaque testis.

Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse.

The androgen receptor CAG repeat polymorphism and modification of breast cancer risk in BRCA1 and BRCA2 mutation carriers.

Segregation of a M404V mutation of the p62/sequestosome 1 (p62/SQSTM1) gene with polyostotic Paget's disease of bone in an Italian family.

A genome-wide survey demonstrates widespread non-linear mRNA in expressed sequences from multiple species.

Improving melanoma classification by integrating genetic and morphologic features.

Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness.

Gene expression and isoform variation analysis using Affymetrix Exon Arrays.

Ovarian cancer has frequent loss of heterozygosity at chromosome 12p12.3-13.1 (region of TEL and Kip1 loci) and chromosome 12q23-ter: evidence for two new tumour-suppressor genes.

Molecular variants of the ATM gene in Hodgkin's disease in children.

Transcription of the human and rodent SPAM1 / PH-20 genes initiates within an ancient endogenous retrovirus.

Analysis of copy number variation using quantitative interspecies competitive PCR.

Multiple epiphyseal dysplasia.

Large-scale trends in the evolution of gene structures within 11 animal genomes.

Alternative splicing and bioinformatic analysis of human U12-type introns.

Core signaling pathways in human pancreatic cancers revealed by global genomic analyses.

Divergence of exonic splicing elements after gene duplication and the impact on gene structures.

Screening of the Fc epsilon RI-beta-gene in a Swiss population of asthmatic children: no association with E237G and identification of new sequence variations.