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 31

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

A sequence-based survey of the complex structural organization of tumor genomes.

PMID 18364049 · PMC2397511 · Genome biology · 2008 · 8 claims · 6 setups

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End sequencing profiling (ESP) can identify all classes of genome rearrangements in tumor genomes by paired-end sequencing of BAC clones

tumors breast bac bt474 bac low-coverage fluorescence
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
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
Molecular tumor profiling: translating genomic insights into clinical advances.

PMID 15287965 · PMC507868 · Genome biology · 2004 · 8 claims · 8 setups

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Gene-expression profiling can distinguish BRCA1- and BRCA2-linked breast tumors from sporadic breast tumors with similar hormone-receptor status

breast ovarian panel tumor gene-expression candidate-gene large-scale
Multiomic analysis of malignant pleural mesothelioma identifies molecular axes and specialized tumor profiles driving intertumor heterogeneity.

PMID 36928603 · PMC10101853 · Nature genetics · 2023 · 8 claims · 6 setups

Has reproduction · 80

The WHO histopathological classification of MPM accounts for only up to ~10% of interpatient molecular differences

mpm mesomics whole-genome bulk methylation
Stage-stratified molecular profiling of non-muscle-invasive bladder cancer enhances biological, clinical, and therapeutic insight.

PMID 35028613 · PMC8714941 · Cell reports. Medicine · 2021 · 8 claims · 8 setups

Has reproduction · 75

Stage-stratified molecular subclassification (analyzing Ta and T1 separately) is more biologically and clinically informative than subtypes derived from all NMIBC combined, especially for T1 tumors.

stage combined patients copy genome-wide targeted
The field of tissue injury in the lung and airway.

PMID 19138985 · PMC2705781 · Cancer prevention research (Philadelphia, Pa.) · 2008 · 8 claims · 8 setups

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Field cancerization and the field of injury reflect molecular changes (genomic, epigenomic, transcriptomic, proteomic) present in histologically normal-appearing tissue distant from and independent of a tumor, throughout the carcinogen-exposed respiratory epithelium

bronchial saliva resected paraffin-embedded whole-genome mtdna methylation-specific
Prostate cancer genomics: towards a new understanding.

PMID 19104501 · PMC2721916 · Nature reviews. Genetics · 2009 · 8 claims · 8 setups

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Multiple GWAS have identified over a dozen replicated germline SNPs each associated with a modest increase in prostate cancer risk

germline families african-american combined genome-wide linkage admixture
Frameshift mutations in coding repeats of protein tyrosine phosphatase genes in colorectal tumors with microsatellite instability.

PMID 19000305 · PMC2586028 · BMC cancer · 2008 · 7 claims · 6 setups

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16 PTP candidate genes containing coding mononucleotide repeats (cMNR) of at least 7 units were identified via bioinformatic analysis and screened in MSI-H cell lines, cancers, and adenomas

msi-h genome colorectal fragment bioinformatic sequencing
Social and ethical implications of genomics, race, ethnicity, and health inequities.

PMID 19000599 · PMC2892396 · Seminars in oncology nursing · 2008 · 8 claims · 5 setups

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Race and ethnicity are increasingly viewed as genetic surrogates for predicting disease risk and treatment response, though directly assessing genomic and environmental factors is more accurate.

population prostate non-small-cell breast genome-wide gene somatic
Single-Cell Transcriptome Analysis Revealed Heterogeneity and Identified Novel Therapeutic Targets for Breast Cancer Subtypes.

PMID 37190091 · PMC10137100 · Cells · 2023 · 8 claims · 8 setups

Has reproduction · 54

Single-cell transcriptomic analysis of EPCAM+Lin- epithelial cells identified unique gene signatures/markers that distinguish ER+, HER2+, ER+HER2+, and TNBC molecular subtypes

breast epcam+cd45-cd8a-cd4-cd19-cd3e cancer identified single-cell differential crispr-cas9
Aberration in DNA methylation in B-cell lymphomas has a complex origin and increases with disease severity.

PMID 23326238 · PMC3542081 · PLoS genetics · 2013 · 8 claims · 8 setups

Has reproduction · 49

B-cell non-Hodgkin lymphomas display striking intra-tumor (intra-sample) and inter-patient (inter-sample) cytosine methylation heterogeneity that increases progressively with disease aggressiveness (NBC<NGC<FL<GCB<ABC).

dlbcl normal same lymphoma help errbs massarray
Array-based profiling of reference-independent methylation status (aPRIMES) identifies frequent promoter methylation and consecutive downregulation of ZIC2 in pediatric medulloblastoma.

PMID 17344319 · PMC1874664 · Nucleic acids research · 2007 · 7 claims · 7 setups

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aPRIMES is a novel array-based method that detects direct (absolute) methylation status of CGIs via competitive hybridization of McrBC-digested (methylated) versus HpaII/BstUI-digested (unmethylated) DNA from the same genome, avoiding reference-tissue and copy-number biases

pediatric tumor eight desmoplastic aprimes bisulfite quantitative
Mutation of ERBB2 provides a novel alternative mechanism for the ubiquitous activation of RAS-MAPK in ovarian serous low malignant potential tumors.

PMID 19010816 · PMC6953412 · Molecular cancer research : MCR · 2008 · 8 claims · 8 setups

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Activating RAS-MAPK pathway mutations are present in >70% of serous LMP tumors versus ~12.5% of serous ovarian carcinomas

serous same lmp braf-mutant gene hotspot erbb2
Genomic profiling of microRNA and messenger RNA reveals deregulated microRNA expression in prostate cancer.

PMID 18676839 · PMC2597340 · Cancer research · 2008 · 8 claims · 7 setups

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MicroRNA processing components (Dicer, DGCR8) and microRNA host genes (MCM7, C9orf5) are significantly up-regulated in prostate tumors versus non-tumor tissue

prostate subset lncap 22rv1 microrna quantitative western
Stemming cancer: functional genomics of cancer stem cells in solid tumors.

PMID 18561035 · PMC2758383 · Stem cell reviews · 2008 · 8 claims · 8 setups

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Cancer stem cells are a minority tumor subpopulation that alone can maintain indefinite tumor growth, as shown by serial transplantation experiments

solid fetal cd133+ breast facs neurosphere genome-wide
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
Histone hyperacetylation disrupts core gene regulatory architecture in rhabdomyosarcoma.

PMID 31784732 · PMC6886578 · Nature genetics · 2019 · 8 claims · 8 setups

Has reproduction · 58

SOX8 is a previously unrecognized core regulatory TF in FP-RMS, co-localizing with other CR TFs at SEs and essential for tumor cell growth

rms rh4 h3k27ac pooled chip-seq
SelTarbase, a database of human mononucleotide-microsatellite mutations and their potential impact to tumorigenesis and immunology.

PMID 19820113 · PMC2808963 · Nucleic acids research · 2010 · 7 claims · 6 setups

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SelTarbase is a curated relational database of published mononucleotide-repeat mutation data from MSI-H human colorectal, gastric, endometrial tumors and colon cancer cell lines.

msi-h aggregated genome mnr sigmoid 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

Experiments

A sequence-based survey of the complex structural organization of tumor genomes.

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

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

Molecular tumor profiling: translating genomic insights into clinical advances.

Multiomic analysis of malignant pleural mesothelioma identifies molecular axes and specialized tumor profiles driving intertumor heterogeneity.

Stage-stratified molecular profiling of non-muscle-invasive bladder cancer enhances biological, clinical, and therapeutic insight.

The field of tissue injury in the lung and airway.

Prostate cancer genomics: towards a new understanding.

Frameshift mutations in coding repeats of protein tyrosine phosphatase genes in colorectal tumors with microsatellite instability.

Social and ethical implications of genomics, race, ethnicity, and health inequities.

Single-Cell Transcriptome Analysis Revealed Heterogeneity and Identified Novel Therapeutic Targets for Breast Cancer Subtypes.

Aberration in DNA methylation in B-cell lymphomas has a complex origin and increases with disease severity.

Array-based profiling of reference-independent methylation status (aPRIMES) identifies frequent promoter methylation and consecutive downregulation of ZIC2 in pediatric medulloblastoma.

Mutation of ERBB2 provides a novel alternative mechanism for the ubiquitous activation of RAS-MAPK in ovarian serous low malignant potential tumors.

Genomic profiling of microRNA and messenger RNA reveals deregulated microRNA expression in prostate cancer.

Stemming cancer: functional genomics of cancer stem cells in solid tumors.

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

Histone hyperacetylation disrupts core gene regulatory architecture in rhabdomyosarcoma.

SelTarbase, a database of human mononucleotide-microsatellite mutations and their potential impact to tumorigenesis and immunology.

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.