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 68

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

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
Detection of the DCC gene product in normal and malignant colorectal tissues and its relation to a codon 201 mutation.

PMID 9484816 · PMC2149930 · British journal of cancer · 1998 · 6 claims · 5 setups

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DCC protein expression is lost in the majority of colorectal tumours while retained in all normal colonic tissue

matched cryosections genomic pcr-rflp rt-pcr northern
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
Enhancing chemotherapy response prediction via matched colorectal tumor-organoid gene expression analysis and network-based biomarker selection.

PMID 39754813 · PMC11754497 · Translational oncology · 2025 · 6 claims · 8 setups

Has reproduction · 78

A consensus WGCNA approach combining matched tumor-organoid and independent organoid drug-response expression data identifies gene modules and hub genes predictive of 5-FU chemotherapy response

colorectal matched combined expression microarray rna-seq consensus
A novel approach for rapid screening of mitochondrial D310 polymorphism.

PMID 16433919 · PMC1388229 · BMC cancer · 2006 · 7 claims · 4 setups

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A single-step BsaXI RFLP assay can rapidly determine 7-C carriers at the D310 first polyC stretch of mtDNA without sequencing

colorectal breast peripheral subset pcr-rflp sanger
Alcohol consumption and breast tumor mitochondrial DNA mutations.

PMID 19847642 · PMC4403627 · Breast cancer research and treatment · 2010 · 8 claims · 6 setups

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Somatic mtDNA mutations are a frequent occurrence in breast tumors

breast paraffin-embedded blood study ttge sequencing immunohistochemistry
Limited clinical relevance of mitochondrial DNA mutation and gene expression analyses in ovarian cancer.

PMID 18842121 · PMC2571110 · BMC cancer · 2008 · 8 claims · 2 setups

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Somatic mutations in the mtDNA D-loop are found in 57% of ovarian cancer samples, mostly C-tract length changes and substitutions

ovarian sanger real-time
Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental design.

PMID 34553212 · PMC8458035 · GigaScience · 2021 · 8 claims · 7 setups

Has reproduction · 87

Genetic variation–based demultiplexing tools can be effectively deployed on cancer scRNA-seq tissue using a pooled experimental design, achieving high recall at acceptable precision-recall tradeoffs in both high-CNV (HGSOC) and high-SNV (lung adenocarcinoma) cancers, even with extremely high doublet proportions.

high-grade lung hgsoc healthy single-cell matched doublet
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
Functional role of the KLF6 tumour suppressor gene in gastric cancer.

PMID 19101139 · PMC2970616 · European journal of cancer (Oxford, England : 1990) · 2009 · 7 claims · 8 setups

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The KLF6 locus undergoes loss of heterozygosity (LOH) in a majority of gastric cancer samples and is associated with advanced tumour stage

gastric ags hs746t fluorescent direct quantitative
Developing a thyroid cancer differentiation state classification system using deep residual networks and metabolic signature profiling.

PMID 40993300 · PMC12460824 · NPJ digital medicine · 2025 · 8 claims · 8 setups

Has reproduction

Metabolic status is closely tied to tumor differentiation state, with distinct metabolic reprogramming occurring during thyroid cancer dedifferentiation

thyroid fuscc gse193581 aggregated untargeted whole-exome transcriptomics
Analysis of the TGF beta functional pathway in epithelial ovarian carcinoma.

PMID 11531253 · PMC2364123 · British journal of cancer · 2001 · 6 claims · 6 setups

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IGFIIR, TGFβ1 and TGFβRII are proposed to function as a unit in the TGFβ growth inhibitory pathway

epithelial tumor genomic ovarian sscp sequencing pcr
Characterisation and protein expression profiling of annexins in colorectal cancer.

PMID 18071363 · PMC2361450 · British journal of cancer · 2008 · 7 claims · 5 setups

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Annexins A1, A2, A4 and A11 are overexpressed in primary colorectal cancer compared with normal colon

dukes colorectal immunised whole-cell gel immunohistochemistry elisa
Expression and mutation analysis of the discoidin domain receptors 1 and 2 in non-small cell lung carcinoma.

PMID 17299390 · PMC2360060 · British journal of cancer · 2007 · 8 claims · 6 setups

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DDR1 is significantly upregulated in NSCLC tumour tissue compared with matched normal lung tissue

nsclc matched lung quantitative pcr genomic
KEGG spider: interpretation of genomics data in the context of the global gene metabolic network.

PMID 19094223 · PMC2646283 · Genome biology · 2008 · 8 claims · 8 setups

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KEGG spider, using a global 'pathway-free' metabolic network framework, provides deeper insight into metabolism variations than existing enrichment-based methods.

diffuse-type liver renal anaplastic differential proteomic proteomics
A small-cell lung cancer genome with complex signatures of tobacco exposure.

PMID 20016488 · PMC2880489 · Nature · 2010 · 8 claims · 7 setups

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22,910 somatic substitutions, including 132 in coding exons, were identified genome-wide in the NCI-H209 SCLC genome.

nci-h209 sclc lu-135 massively pcr multiplex
Prediction of prognostic signatures in triple-negative breast cancer based on the differential expression analysis via NanoString nCounter immune panel.

PMID 33138797 · PMC7607642 · BMC cancer · 2020 · 8 claims · 8 setups

Has reproduction · 72

edgeR-based DEG selection is more appropriate for feature selection than Elastic Net when sample sizes are small.

ffpe same nanostring tnbc nanostring immunohistochemistry differential
iBRIDGE: A Data Integration Method to Identify Inflamed Tumors from Single-cell RNA-Seq Data and Differentiate Cell Type-Specific Markers of Immune-Cell Infiltration.

PMID 37023414 · PMC10236149 · Cancer immunology research · 2023 · 8 claims · 8 setups

Has reproduction · 94

Malignant cells cluster by patient in scRNA-seq data while immune and stromal cells cluster by cell type, making malignant cells uniquely suited to carry patient-level inflamed/cold signal

nsclc coad brca tcga scrna-seq bulk rna-seq
Surfactant protein B gene variations enhance susceptibility to squamous cell carcinoma of the lung in German patients.

PMID 12107845 · PMC2376109 · British journal of cancer · 2002 · 8 claims · 1 setups

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The SP-B intron 4 gene variant is significantly more frequent in squamous cell lung carcinoma (SCC) patients (25.0%) than in matched controls, OR=3.2, P=0.016

peripheral allele-specific
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

Experiments

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

Detection of the DCC gene product in normal and malignant colorectal tissues and its relation to a codon 201 mutation.

Performance of mitochondrial DNA mutations detecting early stage cancer.

Enhancing chemotherapy response prediction via matched colorectal tumor-organoid gene expression analysis and network-based biomarker selection.

A novel approach for rapid screening of mitochondrial D310 polymorphism.

Alcohol consumption and breast tumor mitochondrial DNA mutations.

Limited clinical relevance of mitochondrial DNA mutation and gene expression analyses in ovarian cancer.

Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental design.

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

Functional role of the KLF6 tumour suppressor gene in gastric cancer.

Developing a thyroid cancer differentiation state classification system using deep residual networks and metabolic signature profiling.

Analysis of the TGF beta functional pathway in epithelial ovarian carcinoma.

Characterisation and protein expression profiling of annexins in colorectal cancer.

Expression and mutation analysis of the discoidin domain receptors 1 and 2 in non-small cell lung carcinoma.

KEGG spider: interpretation of genomics data in the context of the global gene metabolic network.

A small-cell lung cancer genome with complex signatures of tobacco exposure.

Prediction of prognostic signatures in triple-negative breast cancer based on the differential expression analysis via NanoString nCounter immune panel.

iBRIDGE: A Data Integration Method to Identify Inflamed Tumors from Single-cell RNA-Seq Data and Differentiate Cell Type-Specific Markers of Immune-Cell Infiltration.

Surfactant protein B gene variations enhance susceptibility to squamous cell carcinoma of the lung in German patients.

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.