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 16

System / cell line: loh ✕ Assay: array ✕ Clear

SiDCoN: a tool to aid scoring of DNA copy number changes in SNP chip data.

PMID 17971856 · PMC2034603 · PloS one · 2007 · 8 claims · 3 setups

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SiDCoN is a spreadsheet-based application that simulates Ballele and logR plots for all known types of DNA copy number change, with or without stromal contamination, for up to 5000 SNP data points and up to 3 combined aberrations

sidcon real mixtures snp re-analysis
Genomic analysis of the clonal origins of relapsed acute lymphoblastic leukemia.

PMID 19039135 · PMC2746051 · Science (New York, N.Y.) · 2008 · 8 claims · 7 setups

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Diagnosis and relapse ALL samples show different patterns of CNAs, with relapse-acquired abnormalities preferentially affecting cell cycle regulation and B-cell development genes

matched bone leukemia diagnosis snp flow quantitative
Decreased expression of the Id3 gene at 1p36.1 in ovarian adenocarcinomas.

PMID 11161400 · PMC2363740 · British journal of cancer · 2001 · 7 claims · 7 setups

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Id3 mRNA and protein expression are decreased in ovarian cancer cell lines compared to immortalized HOSE cells

hose ovarian cdna semi-quantitative northern
SIGMA2: a system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes.

PMID 18840289 · PMC2571113 · BMC bioinformatics · 2008 · 8 claims · 6 setups

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SIGMA2 is a Java-based software system that integrates and visualizes genomic, epigenomic, and transcriptomic cancer data.

single hcc2218 nsclc array gene multi-omics
Search for genomic alterations in monozygotic twins discordant for cleft lip and/or palate.

PMID 19803774 · PMC2893889 · Twin research and human genetics : the official journal of the International Society for Twin Studies · 2009 · 7 claims · 5 setups

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Postzygotic genomic alterations are not a common cause of monozygotic twin discordance for isolated cleft lip and/or palate.

peripheral array custom snp
Loss of heterozygosity at 2q37 in sporadic Wilms' tumor: putative role for miR-562.

PMID 19789318 · PMC2756455 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 8 claims · 8 setups

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2q37 harbors a tumor suppressor gene important in Wilms tumor pathogenesis

sporadic wilms fetal 293t loh multiplex genome-wide
High-resolution array copy number analyses for detection of deletion, gain, amplification and copy-neutral LOH in primary neuroblastoma tumors: four cases of homozygous deletions of the CDKN2A gene.

PMID 18664255 · PMC2527340 · BMC genomics · 2008 · 8 claims · 3 setups

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Affymetrix 50K/250K SNP arrays with CNAG3.0 software provide high-resolution (10-12kb) copy number and allele-specific information suitable for characterizing chromosomal rearrangements in neuroblastoma tumors

neuroblastoma snp multiplex
Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan.

PMID 16420694 · PMC1382255 · BMC bioinformatics · 2006 · 8 claims · 8 setups

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SNPscan is a web-accessible tool that displays SNP copy number, genotype call, and LOH p-value data together in a single plot per sample

lymphoblastoid skin ceph genomic snp array pcr
Recurrent and multiple bladder tumors show conserved expression profiles.

PMID 18590527 · PMC2483988 · BMC cancer · 2008 · 8 claims · 7 setups

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Recurrent and multiple bladder tumors from the same patient display remarkably similar gene expression profiles despite genomic differences.

urothelial genomic tumor processed gene comparative loh
ATBF1 and NQO1 as candidate targets for allelic loss at chromosome arm 16q in breast cancer: absence of somatic ATBF1 mutations and no role for the C609T NQO1 polymorphism.

PMID 18416817 · PMC2377272 · BMC cancer · 2008 · 8 claims · 7 setups

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Five genes (NQO1, ATBF1, DBNDD1, HSBP1, CGI-38) at 16q show significantly lower mRNA expression in breast tumors with LOH at 16q compared to tumors without LOH

ductal same sporadic paired cdna quantitative genotyping
Re-evaluating early breast neoplasia.

PMID 18279539 · PMC2374963 · Breast cancer research : BCR · 2008 · 8 claims · 7 setups

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The classic single linear model of breast cancer progression requires revision based on high-throughput molecular genetic and gene expression data.

dcis breast patient-matched premalignant comparative combined cdna
Pathogenesis of vestibular schwannoma in ring chromosome 22.

PMID 19772601 · PMC2758865 · BMC medical genetics · 2009 · 8 claims · 7 setups

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Tumours in ring chromosome 22 patients arise from the combination of loss of the ring chromosome (first hit) and a pathogenic somatic NF2 mutation on the remaining chromosome 22 (second hit)

peripheral schwann skin-biopsy vestibular karyotyping fish array
Role of FGFR3 in urothelial cell carcinoma: biomarker and potential therapeutic target.

PMID 17912529 · PMC4876910 · World journal of urology · 2007 · 8 claims · 8 setups

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Activating FGFR3 mutations occur frequently in bladder cancer and are strongly associated with low tumour grade and stage

bladder normal urothelial mutation allele-specific laser
p16 mutation spectrum in the premalignant condition Barrett's esophagus.

PMID 19043591 · PMC2585012 · PloS one · 2008 · 8 claims · 6 setups

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44 of 304 Barrett's esophagus patients (14.5%) had p16 mutations (47 total mutations), with a spectrum consistent with oxidative damage and chronic inflammation

flow-sorted esophagectomy endoscopic barrett's sanger flow array
FISH and SNP-A karyotyping in myelodysplastic syndromes: improving cytogenetic detection of del(5q), monosomy 7, del(7q), trisomy 8 and del(20q).

PMID 19758696 · PMC2826525 · Leukemia research · 2010 · 7 claims · 4 setups

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MC, FISH, and SNP-A are complementary techniques whose combined use improves diagnostic yield for detecting del(5q), -7/del(7q), trisomy 8, and del(20q) in MDS

bone pellets extracted cd3+ metaphase fluorescence snp
Two-round coamplification at lower denaturation temperature-PCR (COLD-PCR)-based sanger sequencing identifies a novel spectrum of low-level mutations in lung adenocarcinoma.

PMID 19760750 · PMC2784016 · Human mutation · 2009 · 8 claims · 6 setups

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Two-round fast COLD-PCR followed by Sanger sequencing detects TP53 mutations at abundances as low as ~1%, below the sensitivity of conventional Sanger sequencing (~20-25%)

lung wild-type matched paired two-round real-time airs-rflp

Experiments

SiDCoN: a tool to aid scoring of DNA copy number changes in SNP chip data.

Genomic analysis of the clonal origins of relapsed acute lymphoblastic leukemia.

Decreased expression of the Id3 gene at 1p36.1 in ovarian adenocarcinomas.

SIGMA2: a system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes.

Search for genomic alterations in monozygotic twins discordant for cleft lip and/or palate.

Loss of heterozygosity at 2q37 in sporadic Wilms' tumor: putative role for miR-562.

High-resolution array copy number analyses for detection of deletion, gain, amplification and copy-neutral LOH in primary neuroblastoma tumors: four cases of homozygous deletions of the CDKN2A gene.

Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan.

Recurrent and multiple bladder tumors show conserved expression profiles.

ATBF1 and NQO1 as candidate targets for allelic loss at chromosome arm 16q in breast cancer: absence of somatic ATBF1 mutations and no role for the C609T NQO1 polymorphism.

Re-evaluating early breast neoplasia.

Pathogenesis of vestibular schwannoma in ring chromosome 22.

Role of FGFR3 in urothelial cell carcinoma: biomarker and potential therapeutic target.

p16 mutation spectrum in the premalignant condition Barrett's esophagus.

FISH and SNP-A karyotyping in myelodysplastic syndromes: improving cytogenetic detection of del(5q), monosomy 7, del(7q), trisomy 8 and del(20q).

Two-round coamplification at lower denaturation temperature-PCR (COLD-PCR)-based sanger sequencing identifies a novel spectrum of low-level mutations in lung adenocarcinoma.