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 131

System / cell line: expression ✕ Assay: copy-number ✕ Clear

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
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
Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays.

PMID 17470268 · PMC1868757 · BMC genomics · 2007 · 8 claims · 7 setups

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graCNV uses re-annotated Affymetrix expression microarray probe sets and the WPP algorithm to measure DNA copy number variation at a median resolution of ~17,500 bp without genomic complexity reduction.

neuroblastoma same normal megabladder acgh bac principal
mtDNA depletion confers specific gene expression profiles in human cells grown in culture and in xenograft.

PMID 18980691 · PMC2612029 · BMC genomics · 2008 · 8 claims · 8 setups

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mtDNA depletion confers specific, shared gene expression profiles in A549 cells grown in culture and as xenografts

a549 growth oxygen mtdna
Co-regulation and function of FOXM1/RHNO1 bidirectional genes in cancer.

PMID 33890574 · PMC8104967 · eLife · 2021 · 8 claims · 8 setups

Has reproduction · 76

FOXM1 and RHNO1 are head-to-head bidirectional genes regulated by a shared bidirectional promoter (F/R-BDP)

tcga ft282 gistic expression rt-qpcr
Comprehensive genomic characterization defines human glioblastoma genes and core pathways.

PMID 18772890 · PMC2671642 · Nature · 2008 · 8 claims · 5 setups

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NF1 is a genuine human glioblastoma suppressor gene, inactivated by mutation, deletion, or expression loss in at least 23% of GBM samples

glioblastoma gbm matched sequenced copy gene methylation
Predicting favorable landing pads for targeted integrations in Chinese hamster ovary cell lines by learning stability characteristics from random transgene integrations.

PMID 33304461 · PMC7710658 · Computational and structural biotechnology journal · 2020 · 7 claims · 5 setups

Has reproduction

Expression stability in CHO cell lines is controlled at three levels: choice of integration site, transgene integrity/concatemerization pattern, and stress-related cellular processes.

horizon same cho genome rna-seq targeted
5-methylcytosine RNA modification regulators-based patterns and features of immune microenvironment in acute myeloid leukemia.

PMID 38277218 · PMC10911375 · Aging · 2024 · 8 claims · 8 setups

Has reproduction · 93

m5C regulators are differentially expressed between AML and normal samples and correlate with AML prognosis

tcga aml gse12417 bulk mutation methylation
Alteration of the copy number and deletion of mitochondrial DNA in human hepatocellular carcinoma.

PMID 15150555 · PMC2409531 · British journal of cancer · 2004 · 8 claims · 5 setups

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mtDNA copy number and the content of mitochondrial respiratory proteins are reduced in HCC tumor tissue compared with corresponding non-tumorous liver.

hcc competitive quantitative immunoblot
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
Modified H5 promoter improves stability of insert genes while maintaining immunogenicity during extended passage of genetically engineered MVA vaccines.

PMID 19969118 · PMC2821965 · Vaccine · 2010 · 7 claims · 8 setups

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rMVA expressing multiple antigens under the mH5 promoter exhibit remarkable genetic stability and maintain potent immunogenicity after serial passage

rmva-infected individually bhk-21 pbmc qpcr western southern
Dasatinib resensitizes BRAF/MEK inhibitor efficacy in patient-derived xenografts from patients with progression on BRAF/MEK inhibitor treatment.

PMID 41704766 · PMC12907876 · iScience · 2026 · 8 claims · 6 setups

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Genomic mutation and copy-number status show weak correlation with total/phospho-protein expression and pathway activation in melanoma PDX and TCGA samples

pdx discovery cutaneous nsg reverse-phase targeted rppa
Molecular and Clinical Relevance of ZBTB38 Expression Levels in Prostate Cancer.

PMID 32365491 · PMC7281456 · Cancers · 2020 · 8 claims · 8 setups

Has reproduction · 35

ZBTB38 mRNA expression is significantly lower in prostate cancer than in normal/benign prostate tissue, and further reduced in metastatic versus localised tumours

localised tcga taylor metastatic microarray rna-sequencing clinico-pathological
Differential Gene Expression and Methylation Analysis of Melanoma in TCGA Database to Further Study the Expression Pattern of KYNU in Melanoma.

PMID 35893303 · PMC9329910 · Journal of personalized medicine · 2022 · 8 claims · 8 setups

Has reproduction · 100

Oncogenes MITF, KIT, CDH1, NRAS, AKT1, EGFR, TP53, and CDK4 are elevated while tumor suppressors PTEN, cAMP, and BCL2 are reduced in melanoma

tcga-skcm melanoma-related intradermal keratinocytes rna-seq kegg copy
Deciphering the Immune Microenvironment at the Forefront of Tumor Aggressiveness by Constructing a Regulatory Network with Single-Cell and Spatial Transcriptomic Data.

PMID 38254989 · PMC10815467 · Genes · 2024 · 7 claims · 8 setups

Has reproduction · 85

High expression of transcription factors FOXA1 and EZH2 in malignant cells at the invasive front plays a key role in driving tumor progression

breast er+ epithelial malignant scrna-seq spatial copy
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
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
Discovery of molecular subtypes in leiomyosarcoma through integrative molecular profiling.

PMID 19901961 · PMC2820592 · Oncogene · 2010 · 8 claims · 6 setups

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Unsupervised gene expression clustering identifies 3 reproducible molecular subtypes of LMS (Group I/muscle-enriched, Group II, Group III)

lms independent soft gene array immunohistochemistry
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

Full-text index only

PCDH10 promoter hypermethylation is a frequent event in invasive cervical cancer

invasive lines normal cervical snp methylation-specific bisulphite
Unveiling the NEFH+ malignant cell subtype: Insights from single-cell RNA sequencing in prostate cancer progression and tumor microenvironment interactions.

PMID 39759507 · PMC11695424 · Frontiers in immunology · 2024 · 8 claims · 8 setups

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A malignant cell subtype in PCa with high expression of NEFH was identified, located at the differentiation terminal, showing higher malignancy and association with advanced tumor lesions.

pca malignant tcga mda single-cell infercnv pseudotime

Experiments

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

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

Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays.

mtDNA depletion confers specific gene expression profiles in human cells grown in culture and in xenograft.

Co-regulation and function of FOXM1/RHNO1 bidirectional genes in cancer.

Comprehensive genomic characterization defines human glioblastoma genes and core pathways.

Predicting favorable landing pads for targeted integrations in Chinese hamster ovary cell lines by learning stability characteristics from random transgene integrations.

5-methylcytosine RNA modification regulators-based patterns and features of immune microenvironment in acute myeloid leukemia.

Alteration of the copy number and deletion of mitochondrial DNA in human hepatocellular carcinoma.

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

Modified H5 promoter improves stability of insert genes while maintaining immunogenicity during extended passage of genetically engineered MVA vaccines.

Dasatinib resensitizes BRAF/MEK inhibitor efficacy in patient-derived xenografts from patients with progression on BRAF/MEK inhibitor treatment.

Molecular and Clinical Relevance of ZBTB38 Expression Levels in Prostate Cancer.

Differential Gene Expression and Methylation Analysis of Melanoma in TCGA Database to Further Study the Expression Pattern of KYNU in Melanoma.

Deciphering the Immune Microenvironment at the Forefront of Tumor Aggressiveness by Constructing a Regulatory Network with Single-Cell and Spatial Transcriptomic Data.

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

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

Discovery of molecular subtypes in leiomyosarcoma through integrative molecular profiling.

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

Unveiling the NEFH+ malignant cell subtype: Insights from single-cell RNA sequencing in prostate cancer progression and tumor microenvironment interactions.