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).
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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
A Geniom One-synthesized oligonucleotide microarray can determine the methylation status of individual CpG dinucleotides in parallel, combining high throughput with single-base resolution
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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
CHD5 promoter is highly methylated in neuroblastoma cell lines with 1p deletion and absent CHD5 expression (NLF, IMR5)
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Recovery of bisulfite-converted genomic sequences in the methylation-sensitive QPCR.
PMID 17439964 · PMC1888819 · Nucleic acids research · 2007 · 8 claims · 7 setups
Bisulfite treatment causes DNA strand breakage (via abasic site formation and beta-elimination) in addition to cytosine deamination.
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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
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
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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
MLL-mutant (MLL mu) AML cell lines show significantly lower TSG promoter methylation than MLL wild-type (MLL wt) AML cell lines
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Has reproduction · 76
Co-regulation and function of FOXM1/RHNO1 bidirectional genes in cancer.
PMID 33890574 · PMC8104967 · eLife · 2021 · 8 claims · 8 setups
FOXM1 and RHNO1 are head-to-head bidirectional genes co-amplified and co-expressed in HGSC, regulated by a shared bidirectional promoter (F/R-BDP).
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Has reproduction · 62
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
RHEB promoter hypermethylation is a PCNSL-specific biomarker distinguishing PCNSL from other CNS diseases.
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Has reproduction · 67
Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme.
PMID 27843499 · PMC5105311 · Mobile DNA · 2016 · 6 claims · 7 setups
Canonical (endonuclease-dependent, TPRT-driven) L1 retrotransposition is absent or negligible in GBM tumours and cultured GBM cell lines
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Has reproduction · 49
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
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).
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Downregulation of death-associated protein kinase 1 (DAPK1) in chronic lymphocytic leukemia.
PMID 17540169 · PMC4647864 · Cell · 2007 · 8 claims · 13 setups
DAPK1 promoter is epigenetically silenced by DNA methylation in almost all sporadic CLL cases
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MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome.
PMID 19906696 · PMC2811030 · Nucleic acids research · 2010 · 6 claims · 4 setups
MiGS combines MBD2 MBD-domain precipitation of methylated DNA with massively parallel sequencing to enable unbiased, high-throughput genome-wide DNA methylation profiling
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Genome-wide tracking of unmethylated DNA Alu repeats in normal and cancer cells.
PMID 18084025 · PMC2241897 · Nucleic acids research · 2008 · 5 claims · 7 setups
QUMA (quantitative real-time PCR) and AUMA (fingerprinting PCR) methods can quantify and individually identify unmethylated Alu elements on a genomic scale using the methylation-sensitive SmaI site as a surrogate marker
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Identification of the imprinted KLF14 transcription factor undergoing human-specific accelerated evolution.
PMID 17480121 · PMC1865561 · PLoS genetics · 2007 · 7 claims · 8 setups
KLF14 is a novel imprinted gene showing monoallelic maternal expression in embryonic and extra-embryonic tissues of both human and mouse
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Has reproduction · 78
TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells.
PMID 23233547 · PMC3589534 · Genome research · 2013 · 8 claims · 8 setups
TRIM28 repression of ERVs protects cellular gene expression in early embryos from perturbation by cis-acting activators contained within these retroelements.
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1p36 is a preferential target of chromosome 1 deletions in astrocytic tumours and homozygously deleted in a subset of glioblastomas.
PMID 17934521 · PMC2650419 · Oncogene · 2008 · 8 claims · 8 setups
Total 1p deletion is rare (2%) in astrocytic tumours, whereas partial deletions involving 1p36 are common and increase with malignancy grade (22% in anaplastic astrocytomas, 34% in glioblastomas)
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Loss of heterozygosity at 2q37 in sporadic Wilms' tumor: putative role for miR-562.
PMID 19789318 · PMC2756455 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 8 claims · 8 setups
2q37 harbors a tumor suppressor gene important in Wilms tumor pathogenesis