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 52

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

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
CpG island methylation status and mutation analysis of the RB1 gene essential promoter region and protein-binding pocket domain in nervous system tumours.

PMID 12556968 · PMC2376780 · British journal of cancer · 2003 · 8 claims · 4 setups

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RB1 CpG island hypermethylation is a common epigenetic event associated with development of malignant nervous system tumours

nervous bisulphite-modified same pcr-sscp methylation-specific bisulphite
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
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
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
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
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
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
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 alterations of Ras signalling pathway in colorectal neoplasia: analysis based on tumour clinicopathological features.

PMID 17923875 · PMC2360240 · British journal of cancer · 2007 · 8 claims · 4 setups

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K-ras/BRAF mutations and RASSF2 methylation frequently co-occur in colorectal adenomas, suggesting synergistic cooperation

colorectal clinicopathological direct combined histopathological
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
Alterations in candidate genes PHF2, FANCC, PTCH1 and XPA at chromosomal 9q22.3 region: pathological significance in early- and late-onset breast carcinoma.

PMID 18990233 · PMC2633285 · Molecular cancer · 2008 · 8 claims · 5 setups

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PHF2, FANCC and PTCH1 show high frequency of alterations (deletion/methylation) compared to XPA in both early- and late-onset breast carcinoma groups

invasive breast normal microsatellite methylation sscp
Microsatellite instability and mismatch repair gene inactivation in sporadic pancreatic and colon tumours.

PMID 10389971 · PMC2363009 · British journal of cancer · 1999 · 6 claims · 5 setups

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Microsatellite instability is common in sporadic pancreatic cancer but occurs at a uniformly low rate and is not accompanied by hMLH1/hMSH2 alterations, suggesting it does not drive pancreatic tumorigenesis.

sporadic msi-positive tumour unstable microsatellite denaturing sequencing
Pancreatic tumours: molecular pathways implicated in ductal cancer are involved in ampullary but not in exocrine nonductal or endocrine tumorigenesis.

PMID 11161385 · PMC2363700 · British journal of cancer · 2001 · 8 claims · 6 setups

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PDC shows frequent alterations of K-ras, p53, p16 and DPC4, confirming these as the core molecular fingerprint of ductal cancer

pancreatic same tumor pet sscp methylation-specific microsatellite
Genetic and epigenetic changes in primary metastatic and nonmetastatic colorectal cancer.

PMID 16969349 · PMC2360724 · British journal of cancer · 2006 · 8 claims · 8 setups

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K-Ras codon 12 mutations are significantly associated with metastatic (M+) CRC

crc 202-patient pcr-rflp sscp immunohistochemistry
BRAF, KRAS and PIK3CA mutations in colorectal serrated polyps and cancer: primary or secondary genetic events in colorectal carcinogenesis?

PMID 18782444 · PMC2553419 · BMC cancer · 2008 · 8 claims · 7 setups

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KRAS, BRAF and PIK3CA mutations occur in the majority of colorectal polyps and are mutually exclusive

formalin-fixed colorectal sporadic polyps pcr bisulfite pentaplex
Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme.

PMID 27843499 · PMC5105311 · Mobile DNA · 2016 · 6 claims · 7 setups

Has reproduction · 67

Canonical (endonuclease-dependent, TPRT-driven) L1 retrotransposition is absent or negligible in GBM tumours and cultured GBM cell lines

brain tumour gbm retrotransposon empty qrt-pcr
MSH6 missense mutations are often associated with no or low cancer susceptibility.

PMID 15354210 · PMC2409912 · British journal of cancer · 2004 · 7 claims · 8 setups

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Most MSH6 missense changes found in MSI-positive tumours are likely clinically innocent or of low cancer-susceptibility significance

microdissected blood individuals paraffin-embedded microsatellite exon sscp
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
CHEK2 mutations affecting kinase activity together with mutations in TP53 indicate a functional pathway associated with resistance to epirubicin in primary breast cancer.

PMID 18725978 · PMC2518116 · PloS one · 2008 · 7 claims · 6 setups

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TP53 mutations, especially those affecting the L2/L3 DNA-binding domains, are associated with resistance (progressive disease) to epirubicin therapy

snap-frozen tumor u-2-os patients pcr bisulphite loss

Experiments

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

CpG island methylation status and mutation analysis of the RB1 gene essential promoter region and protein-binding pocket domain in nervous system tumours.

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

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

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

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

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

DNA demethylation is associated with malignant progression of lower-grade gliomas.

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

Genetic and epigenetic alterations of Ras signalling pathway in colorectal neoplasia: analysis based on tumour clinicopathological features.

DNA methylation of cancer genome.

Alterations in candidate genes PHF2, FANCC, PTCH1 and XPA at chromosomal 9q22.3 region: pathological significance in early- and late-onset breast carcinoma.

Microsatellite instability and mismatch repair gene inactivation in sporadic pancreatic and colon tumours.

Pancreatic tumours: molecular pathways implicated in ductal cancer are involved in ampullary but not in exocrine nonductal or endocrine tumorigenesis.

Genetic and epigenetic changes in primary metastatic and nonmetastatic colorectal cancer.

BRAF, KRAS and PIK3CA mutations in colorectal serrated polyps and cancer: primary or secondary genetic events in colorectal carcinogenesis?

Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme.

MSH6 missense mutations are often associated with no or low cancer susceptibility.

The field of tissue injury in the lung and airway.

CHEK2 mutations affecting kinase activity together with mutations in TP53 indicate a functional pathway associated with resistance to epirubicin in primary breast cancer.