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 30

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

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
High DNA methylation age deceleration defines an aggressive phenotype with immunoexclusion environments in endometrial carcinoma.

PMID 37388735 · PMC10303802 · Frontiers in immunology · 2023 · 8 claims · 8 setups

Has reproduction · 76

Almost 90% of TCGA EC tumors exhibit DNA methylation age deceleration (DNAmad) relative to patient chronological age as assessed by the Horvath clock

tumors metastatic methylation bulk kegg
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
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
Genomic and mutational profiling to assess clonal relationships between multiple non-small cell lung cancers.

PMID 19671847 · PMC2892178 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 8 claims · 5 setups

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Genomic profiling by aCGH can distinguish clonal tumors from independent primaries with high confidence by identifying matching versus non-matching regions of allelic gain/loss.

fresh-frozen same banked resected array mutational pcr
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
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
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
An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer.

PMID 19012953 · PMC2990916 · Cell · 2008 · 7 claims · 8 setups

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shRNA pools targeting genes recurrently deleted in human HCC accelerate hepatocarcinogenesis in vivo, whereas randomly selected shRNA pools do not.

hepatocellular p53 genomic hepatoma array-based pooled shrna
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
DNA demethylation is associated with malignant progression of lower-grade gliomas.

PMID 30760837 · PMC6374451 · Scientific reports · 2019 · 8 claims · 8 setups

Has reproduction

Nearly half of IDH-mutant glioblastomas that progressed from lower-grade gliomas show characteristic partial DNA demethylation in previously methylated (G-CIMP) genomic regions of their initial tumor.

gliomas neural analysis tcga methylation whole-exome sequencing
Functional copy-number alterations in cancer.

PMID 18784837 · PMC2527508 · PloS one · 2008 · 8 claims · 3 setups

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RAE is a comprehensive computational framework that robustly maps chromosomal alterations in tumor samples and statistically assesses their functional importance in cancer.

pleomorphic hapmap large snp computational
Exploiting noise in array CGH data to improve detection of DNA copy number change.

PMID 17272296 · PMC1994778 · Nucleic acids research · 2007 · 7 claims · 4 setups

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When aberrations are present, noise in BAC, 19k oligo, and 385k oligo array-CGH data is highly non-Gaussian and shows long-range spatial correlations.

atm-deficient normal simulated array simulated
Widespread dysregulation of MiRNAs by MYCN amplification and chromosomal imbalances in neuroblastoma: association of miRNA expression with survival.

PMID 19924232 · PMC2773120 · PloS one · 2009 · 8 claims · 5 setups

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37 miRNAs are significantly differentially expressed between MYCN-amplified (MNA) and non-MNA neuroblastoma tumors, suggesting direct or indirect regulation by MYCN

neuroblastoma shep-tet21 stem-loop array tlda
Comprehensive genomic analysis reveals clinically relevant molecular distinctions between thymic carcinomas and thymomas.

PMID 19861435 · PMC2783876 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 7 claims · 7 setups

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Comprehensive genomic analysis shows thymic carcinomas are molecularly distinct from thymomas

resected thymic previously mass dideoxynucleotide array
Oncogene mutations, copy number gains and mutant allele specific imbalance (MASI) frequently occur together in tumor cells.

PMID 19826477 · PMC2757721 · PloS one · 2009 · 8 claims · 8 setups

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Homozygous mutations of oncogenes are frequent (20%) across 833 cancer cell lines of 12 tumor types in the Sanger database

tumors cancer tumor lung direct database quantitative
A statistical approach for array CGH data analysis.

PMID 15705208 · PMC549559 · BMC bioinformatics · 2005 · 8 claims · 4 setups

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Existing model-selection criteria (AIC, BIC, and prior ad hoc penalties) are not well adapted to estimating the number of segments in array CGH data

fibroblast simulated bt474 dissected array numerical
Oncogenic mutations in GNAQ occur early in uveal melanoma.

PMID 18719078 · PMC2634606 · Investigative ophthalmology & visual science · 2008 · 8 claims · 7 setups

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Activating GNAQ mutations at codon 209 occur in 33/67 (49%) of primary uveal melanomas, making it the most common known oncogenic mutation in UM

uveal peripheral normal well-characterized pcr sequencing array-based
An integrative genomic and proteomic analysis of PIK3CA, PTEN, and AKT mutations in breast cancer.

PMID 18676830 · PMC2680495 · Cancer research · 2008 · 8 claims · 5 setups

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PIK3CA mutations are more common in hormone receptor-positive and HER2-positive tumors than in basal-like breast cancers

breast hormone early-stage mass sanger reverse-phase
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

Experiments

Recurrent and multiple bladder tumors show conserved expression profiles.

High DNA methylation age deceleration defines an aggressive phenotype with immunoexclusion environments in endometrial carcinoma.

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

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

Genomic and mutational profiling to assess clonal relationships between multiple non-small cell lung cancers.

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.

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

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

An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer.

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

DNA demethylation is associated with malignant progression of lower-grade gliomas.

Functional copy-number alterations in cancer.

Exploiting noise in array CGH data to improve detection of DNA copy number change.

Widespread dysregulation of MiRNAs by MYCN amplification and chromosomal imbalances in neuroblastoma: association of miRNA expression with survival.

Comprehensive genomic analysis reveals clinically relevant molecular distinctions between thymic carcinomas and thymomas.

Oncogene mutations, copy number gains and mutant allele specific imbalance (MASI) frequently occur together in tumor cells.

A statistical approach for array CGH data analysis.

Oncogenic mutations in GNAQ occur early in uveal melanoma.

An integrative genomic and proteomic analysis of PIK3CA, PTEN, and AKT mutations in breast cancer.

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.