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 9

System / cell line: fibroblast ✕ Assay: tumor ✕ Clear

A gene encoding antigenic peptides of human squamous cell carcinoma recognized by cytotoxic T lymphocytes.

PMID 9449708 · PMC2212124 · The Journal of experimental medicine · 1998 · 8 claims · 8 setups

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A gene, SART-1, encoding antigenic peptides recognized by HLA-A2601-restricted CTLs was identified from human squamous cell carcinoma cells.

ke4 normal pbmcs va13 expression northern western
Intrinsic genetic characteristics determine tumor-modifying capacity of fibroblasts: matrix metalloproteinase-3 5A/5A genotype enhances breast cancer cell invasion.

PMID 17922906 · PMC2242664 · Breast cancer research : BCR · 2007 · 8 claims · 8 setups

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Tumor-derived fibroblasts promote higher levels of breast cancer cell invasion than normal fibroblasts

breast conditioned mda-mb-468 genomic invasion immunofluorescence pcr-rflp
Independent component analysis reveals new and biologically significant structures in micro array data.

PMID 16762055 · PMC1557674 · BMC bioinformatics · 2006 · 7 claims · 8 setups

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ICA applied to three microarray datasets reveals many biologically significant components, including low-ranking ones not obvious by rank alone

acute serum-stimulated head aml microarray clust term
An individualized causal framework for learning intercellular communication networks that define microenvironments of individual tumors.

PMID 36548438 · PMC9822106 · PLoS computational biology · 2022 · 8 claims · 7 setups

Has reproduction · 67

An individualized causal analysis framework can discover tumor-specific intercellular communication networks (ICNs) from transcriptomic data

hnscc pooled cd45+ cd8+ single-cell nhdp celda
Identification and validation of a metabolic-related gene risk model predicting the prognosis of lung, colon, and breast cancers.

PMID 39779736 · PMC11711664 · Scientific reports · 2025 · 8 claims · 8 setups

Has reproduction · 74

540 DEGs overlap across breast, colorectal, and lung cancers out of 11,384 DEGs analyzed

breast colorectal lung common microarray kegg protein-protein
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
Downregulation of Splicing Factor PTBP1 Curtails FBXO5 Expression to Promote Cellular Senescence in Lung Adenocarcinoma.

PMID 39057099 · PMC11276454 · Current issues in molecular biology · 2024 · 8 claims · 8 setups

Has reproduction · 59

PTBP1 is significantly upregulated across multiple cancer types including LUAD, and higher PTBP1 levels are associated with worse LUAD patient survival

cancer luad fibroblast a549 pan-cancer differential replicative
A statistical change point model approach for the detection of DNA copy number variations in array CGH data.

PMID 19875853 · PMC4154476 · IEEE/ACM transactions on computational biology and bioinformatics · 2009 · 7 claims · 4 setups

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A novel mean and variance change point model (MVCM) is proposed to detect CNVs/breakpoints in aCGH data.

simulated fibroblast breast simulation array
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

Experiments

A gene encoding antigenic peptides of human squamous cell carcinoma recognized by cytotoxic T lymphocytes.

Intrinsic genetic characteristics determine tumor-modifying capacity of fibroblasts: matrix metalloproteinase-3 5A/5A genotype enhances breast cancer cell invasion.

Independent component analysis reveals new and biologically significant structures in micro array data.

An individualized causal framework for learning intercellular communication networks that define microenvironments of individual tumors.

Identification and validation of a metabolic-related gene risk model predicting the prognosis of lung, colon, and breast cancers.

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

Downregulation of Splicing Factor PTBP1 Curtails FBXO5 Expression to Promote Cellular Senescence in Lung Adenocarcinoma.

A statistical change point model approach for the detection of DNA copy number variations in array CGH data.

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.