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 81

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

Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays.

PMID 19903341 · PMC2810663 · Genome biology · 2009 · 7 claims · 3 setups

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GAP is a method for automatic detection of absolute segmental copy number and genotype status from SNP-array cancer genome profiles

breast snp flow karyotyping
Identifying alternative hyper-splicing signatures in MG-thymoma by exon arrays.

PMID 18545673 · PMC2409220 · PloS one · 2008 · 8 claims · 6 setups

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An integrative ad-hoc functional GO analysis combining threshold-based (Fisher exact/hypergeometric) and threshold-free (Kolmogorov-Smirnov) statistics, plus term-to-parent comparisons, detects disease-relevant splicing events from exon array data.

mg-thymoma colon exon fluorescent reverse
SIGMA: a system for integrative genomic microarray analysis of cancer genomes.

PMID 17192189 · PMC1764892 · BMC genomics · 2006 · 7 claims · 6 setups

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SIGMA is a user-friendly, web-based Java application for visualization and integrative analysis of array CGH data across multiple platforms.

cancer lung breast array medip segmentation
Identification of novel gene amplifications in breast cancer and coexistence of gene amplification with an activating mutation of PIK3CA.

PMID 19706770 · PMC2745517 · Cancer research · 2009 · 8 claims · 8 setups

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Genome-wide DNA copy number analysis of 161 primary breast tumors identified six novel focally amplified genes: POLD3, IRAK4, IRX2, TBL1XR1, ASPH, and BRD4

breast mcf10a mcf10ca1h snp quantitative rt-qpcr
Integrative genomics analysis of chromosome 5p gain in cervical cancer reveals target over-expressed genes, including Drosha.

PMID 18559093 · PMC2440550 · Molecular cancer · 2008 · 7 claims · 6 setups

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Gain of chromosome 5p is the most frequent genomic alteration in invasive cervical cancer

cervical tumors pap tumor snp fluorescence fish
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
The diagnosis and management of pre-invasive breast disease: promise of new technologies in understanding pre-invasive breast lesions.

PMID 14580250 · PMC314415 · Breast cancer research : BCR · 2003 · 8 claims · 8 setups

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ADH and ductal carcinoma in situ (DCIS) are precursor lesions molecularly similar to adjacent invasive breast cancer

locally adh brca1 malignant array chromosome-based cdna
Somatic mutations of the Parkinson's disease-associated gene PARK2 in glioblastoma and other human malignancies.

PMID 19946270 · PMC4002225 · Nature genetics · 2010 · 8 claims · 8 setups

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PARK2 is a frequently and specifically targeted gene within recurrent 6q25.2-q27 copy number losses in glioblastoma and colon cancer

colon gbm cancer dbtrg array pcr colony
Hierarchical classification-based pan-cancer methylation analysis to classify primary cancer.

PMID 38066424 · PMC10709847 · BMC bioinformatics · 2023 · 8 claims · 5 setups

Has reproduction · 83

CHCT, a hierarchical classification tool, splits classification of 30 cancer types into ten smaller subproblems using a two-tier architecture to classify primary cancer by methylation profile

cancer clinical training independent methylation upgma random
Performance of mitochondrial DNA mutations detecting early stage cancer.

PMID 18834532 · PMC2572633 · BMC cancer · 2008 · 8 claims · 6 setups

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The Affymetrix MitoChip resequencing array is a high-throughput, higher-resolution alternative to capillary sequencing for detecting mtDNA point mutations and heteroplasmy in clinical specimens.

matched blood mtdna low-quantity mitochondrial capillary str
High-resolution array comparative genomic hybridization of single micrometastatic tumor cells.

PMID 18344524 · PMC2367728 · Nucleic acids research · 2008 · 7 claims · 8 setups

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A protocol combining PCR-based whole genome amplification with arrays of highly purified BAC clones enables detection of DNA copy number changes in single cells

single bac amplified pi-scei array quantitative dot
Reduced 5-FU clearance in a patient with low DPD activity due to heterozygosity for a mutant allele of the DPYD gene.

PMID 11953843 · PMC2364178 · British journal of cancer · 2002 · 7 claims · 5 setups

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Heterozygosity for the IVS14+1G>A DPYD splice-site mutation is associated with markedly reduced 5-FU clearance and severe 5-FU toxicity in the index patient.

plasma peripheral pbm genomic reversed-phase pharmacokinetic dpd
MMASS: an optimized array-based method for assessing CpG island methylation.

PMID 17041235 · PMC1635254 · Nucleic acids research · 2006 · 8 claims · 7 setups

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MMASS-v2 (optimized AciI/HinP1I/HpyCH4IV/HpaII enzyme combination with McrBC digestion) offers improved sensitivity and statistical power for microarray-based CpG island methylation detection compared to MMASS-v1, MMASS-sub and the Nouzova method

hct116 sssi-methylated hcgi12k methylation spike-in cobra
High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer.

PMID 17925008 · PMC2246289 · Genome biology · 2007 · 7 claims · 8 setups

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A novel subtype of high-grade ER-negative breast cancer exists, characterized by a low genomic instability index (GII)

breast computational array-cgh gene bac
"Sequencing-grade" screening for BRCA1 variants by oligo-arrays.

PMID 18973698 · PMC2583995 · Journal of translational medicine · 2008 · 7 claims · 6 setups

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An oligo-array platform can detect BRCA1 SNPs, insertions, and deletions of known and unknown variants, including in heterozygous conditions, with accuracy comparable to direct sequencing

genomic pcr mcf-10a brca1 oligo-nucleotide direct pcr
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
Protocadherin PCDH10, involved in tumor progression, is a frequent and early target of promoter hypermethylation in cervical cancer.

PMID 19681120 · PMC3430375 · Genes, chromosomes & cancer · 2009 · 8 claims · 5 setups

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PCDH10 promoter hypermethylation is a frequent event in invasive cervical cancer

invasive lines normal cervical snp methylation-specific bisulphite
Gene-expression patterns in peripheral blood classify familial breast cancer susceptibility.

PMID 26538066 · PMC4634735 · BMC medical genomics · 2015 · 8 claims · 5 setups

Has reproduction · 83

A multigene peripheral-blood gene-expression biomarker accurately classifies which women from high-risk families develop familial breast cancer.

peripheral pbmcs blood normal gene-expression lymphocyte gene
Inactivation of O6-methylguanine-DNA methyltransferase by promoter CpG island hypermethylation in gastric cancers.

PMID 12085181 · PMC2375420 · British journal of cancer · 2002 · 6 claims · 8 setups

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Loss of MGMT expression in gastric carcinomas frequently results from promoter CpG island hypermethylation.

gastric consecutive snu-620 methylation-specific immunohistochemistry western
The use of whole genome amplification to study chromosomal changes in prostate cancer: insights into genome-wide signature of preneoplasia associated with cancer progression.

PMID 16573809 · PMC1450280 · BMC genomics · 2006 · 7 claims · 8 setups

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MDA-amplified DNA does not introduce major distortion of copy number imbalance assignments compared to unamplified DNA in control CGH experiments.

laser-capture-microdissected normal cancer fresh-frozen array gacgh laser

Experiments

Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays.

Identifying alternative hyper-splicing signatures in MG-thymoma by exon arrays.

SIGMA: a system for integrative genomic microarray analysis of cancer genomes.

Identification of novel gene amplifications in breast cancer and coexistence of gene amplification with an activating mutation of PIK3CA.

Integrative genomics analysis of chromosome 5p gain in cervical cancer reveals target over-expressed genes, including Drosha.

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

The diagnosis and management of pre-invasive breast disease: promise of new technologies in understanding pre-invasive breast lesions.

Somatic mutations of the Parkinson's disease-associated gene PARK2 in glioblastoma and other human malignancies.

Hierarchical classification-based pan-cancer methylation analysis to classify primary cancer.

Performance of mitochondrial DNA mutations detecting early stage cancer.

High-resolution array comparative genomic hybridization of single micrometastatic tumor cells.

Reduced 5-FU clearance in a patient with low DPD activity due to heterozygosity for a mutant allele of the DPYD gene.

MMASS: an optimized array-based method for assessing CpG island methylation.

High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer.

"Sequencing-grade" screening for BRCA1 variants by oligo-arrays.

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

Protocadherin PCDH10, involved in tumor progression, is a frequent and early target of promoter hypermethylation in cervical cancer.

Gene-expression patterns in peripheral blood classify familial breast cancer susceptibility.

Inactivation of O6-methylguanine-DNA methyltransferase by promoter CpG island hypermethylation in gastric cancers.

The use of whole genome amplification to study chromosomal changes in prostate cancer: insights into genome-wide signature of preneoplasia associated with cancer progression.