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 34

System / cell line: lines ✕ Assay: methylation ✕ Clear

Hypomethylation and expression of BEX2, IGSF4 and TIMP3 indicative of MLL translocations in acute myeloid leukemia.

PMID 19835597 · PMC2770485 · Molecular cancer · 2009 · 8 claims · 8 setups

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MLL-mutant (MLL mu) AML cell lines show significantly lower TSG promoter methylation than MLL wild-type (MLL wt) AML cell lines

acute mll lines bone ms-mlpa hhai methylation-specific
Increased prevalence of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer.

PMID 38974967 · PMC11225361 · iScience · 2024 · 7 claims · 7 setups

Has reproduction · 95

Luminal breast cancer gene expression signature is closely/positively associated with an epithelial signature

breast-cancer-specific tcga ccle four single-sample survival genome-wide
CHD5, a tumor suppressor gene deleted from 1p36.31 in neuroblastomas.

PMID 18577749 · PMC2483574 · Journal of the National Cancer Institute · 2008 · 7 claims · 8 setups

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CHD5 promoter is highly methylated in neuroblastoma cell lines with 1p deletion and absent CHD5 expression (NLF, IMR5)

neuroblastoma nlf athymic methylation-specific quantitative soft
Recovery of bisulfite-converted genomic sequences in the methylation-sensitive QPCR.

PMID 17439964 · PMC1888819 · Nucleic acids research · 2007 · 8 claims · 7 setups

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Bisulfite treatment causes DNA strand breakage (via abasic site formation and beta-elimination) in addition to cytosine deamination.

genomic synthetic bisulfite-treated cloned methylation-sensitive quantitative gel
Aberrations of the p14(ARF) and p16(INK4a) genes in renal cell carcinomas.

PMID 11749694 · PMC5926680 · Japanese journal of cancer research : Gann · 2001 · 7 claims · 6 setups

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Homozygous co-deletion of p14ARF and p16INK4a is frequent in RCC cell lines (5 of 6 lines)

rcc differential methylation-specific immunohistochemistry
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
Array-based analysis of genomic DNA methylation patterns of the tumour suppressor gene p16INK4A promoter in colon carcinoma cell lines.

PMID 15860770 · PMC1087791 · Nucleic acids research · 2005 · 8 claims · 4 setups

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A Geniom One-synthesized oligonucleotide microarray can determine the methylation status of individual CpG dinucleotides in parallel, combining high throughput with single-base resolution

hct116 p16 genomic methylation-specific combined oligonucleotide
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
Specific Marker Gene Analysis for Primary Central Nervous System Lymphoma Based on Methylation Difference and Development of Detection Primers.

PMID 41097902 · PMC12528802 · Brain and behavior · 2025 · 6 claims · 6 setups

Has reproduction · 62

RHEB promoter hypermethylation is a PCNSL-specific biomarker distinguishing PCNSL from other CNS diseases.

datasets cns tcga gdc 450k rrbs roc
Pleiotropic effects of MORC2 derive from its epigenetic signature.

PMID 40302207 · PMC12782172 · Brain : a journal of neurology · 2026 · 8 claims · 8 setups

Has reproduction

A MORC2-specific DNA methylation episignature exists that is universal across all MORC2-associated phenotypes and conserved across blood and fibroblast tissue

blood fibroblasts fibroblast patient-derived methylation svm phenotype-specific
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
Genetic and epigenetic changes in the common 1p36 deletion in neuroblastoma tumours.

PMID 17940511 · PMC2360241 · British journal of cancer · 2007 · 8 claims · 4 setups

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Treatment of neuroblastoma cell lines with the HDAC inhibitor trichostatin A (TSA) increased transcription of ERRFI1, PIK3CD, RBP7 and CASZ1, indicating possible epigenetic downregulation of these genes in NB

lines tumours real-time bisulphite sequencing
Downregulation of death-associated protein kinase 1 (DAPK1) in chronic lymphocytic leukemia.

PMID 17540169 · PMC4647864 · Cell · 2007 · 8 claims · 13 setups

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DAPK1 promoter is epigenetically silenced by DNA methylation in almost all sporadic CLL cases

cd19+ leukemia raji jurkat quantitative cobra chromatin
Convergence of mutation and epigenetic alterations identifies common genes in cancer that predict for poor prognosis.

PMID 18507500 · PMC2429944 · PLoS medicine · 2008 · 7 claims · 7 setups

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At least 36 of the 189 newly mutated CAN genes are targets of promoter CpG island hypermethylation, often in both colon and breast cancer cell lines

breast same selected hct116 expression methylation-specific rt-pcr
DNA methylation of cancer genome.

PMID 19960550 · PMC2940836 · Birth defects research. Part C, Embryo today : reviews · 2009 · 8 claims · 7 setups

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Cancer epigenome alterations fall into two main categories: hypermethylation of tumor suppressor genes and hypomethylation of oncogenes or heterochromatin.

embryonic germ heterozygous cancer gene hypomorphic methyltransferase
Genetic and epigenetic analyses of MBD3 in colon and lung cancer.

PMID 15138480 · PMC2410281 · British journal of cancer · 2004 · 7 claims · 5 setups

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MBD3 is not a major target of genetic or epigenetic alteration in colon and lung cancer

colon normal pcr-sscp rt-pcr northern
SIGMA: a system for integrative genomic microarray analysis of cancer genomes.

PMID 17192189 · PMC1764892 · BMC genomics · 2006 · 7 claims · 6 setups

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SIGMA is a user-friendly, web-based Java application for visualization and integrative analysis of array CGH data across multiple platforms.

cancer lung breast array medip segmentation
Functional epigenomics approach to identify methylated candidate tumour suppressor genes in renal cell carcinoma.

PMID 18195710 · PMC2361461 · British journal of cancer · 2008 · 8 claims · 4 setups

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HAI-2/SPINT2 was previously identified as a novel epigenetically inactivated candidate RCC tumour suppressor gene

rcc skrc39 gene rt-pcr bisulphite
PredTAD: A machine learning framework that models 3D chromatin organization alterations leading to oncogene dysregulation in breast cancer cell lines.

PMID 34093998 · PMC8142020 · Computational and structural biotechnology journal · 2021 · 7 claims · 8 setups

Has reproduction · 77

PredTAD, a Gradient Boosting Machine model using epigenomic and genomic features plus neighboring-bin information, classifies 10 kb genomic regions as TAD boundary or non-boundary across normal and breast cancer cell lines.

mcf10a t47d gm12878 mcf7 hi-c chip-seq atac-seq

Experiments

Hypomethylation and expression of BEX2, IGSF4 and TIMP3 indicative of MLL translocations in acute myeloid leukemia.

Increased prevalence of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer.

CHD5, a tumor suppressor gene deleted from 1p36.31 in neuroblastomas.

Recovery of bisulfite-converted genomic sequences in the methylation-sensitive QPCR.

Aberrations of the p14(ARF) and p16(INK4a) genes in renal cell carcinomas.

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

Array-based analysis of genomic DNA methylation patterns of the tumour suppressor gene p16INK4A promoter in colon carcinoma cell lines.

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.

Specific Marker Gene Analysis for Primary Central Nervous System Lymphoma Based on Methylation Difference and Development of Detection Primers.

Pleiotropic effects of MORC2 derive from its epigenetic signature.

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

Genetic and epigenetic changes in the common 1p36 deletion in neuroblastoma tumours.

Downregulation of death-associated protein kinase 1 (DAPK1) in chronic lymphocytic leukemia.

Convergence of mutation and epigenetic alterations identifies common genes in cancer that predict for poor prognosis.

DNA methylation of cancer genome.

Genetic and epigenetic analyses of MBD3 in colon and lung cancer.

SIGMA: a system for integrative genomic microarray analysis of cancer genomes.

Functional epigenomics approach to identify methylated candidate tumour suppressor genes in renal cell carcinoma.

PredTAD: A machine learning framework that models 3D chromatin organization alterations leading to oncogene dysregulation in breast cancer cell lines.