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).

• Methods for genome-wide analysis of DNA methylation in intestinal tumors.

  PMID 19854208 · PMC2891386 · Mutation research · 2010 · 8 claims · 8 setups

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  Aberrant DNA methylation, including CpG island hypermethylation of tumor suppressors and genome-wide hypomethylation, is strongly linked to the origin and progression of colorectal cancer.

  cd19+ lung gpx1 tumor mira medip goldengate

• Computationally scalable regression modeling for ultrahigh-dimensional omics data with ParProx.

  PMID 34254998 · PMC8575036 · Briefings in bioinformatics · 2021 · 6 claims · 4 setups

  Has reproduction · 79

  ParProx implements latent group lasso penalized regression (overlapping and non-overlapping groups) for survival (Cox) and classification (logistic) analysis of omics data.

  tcga breast liver simulated cox logistic simulation

• 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

• DNA methylation and mRNA expression of SYN III, a candidate gene for schizophrenia.

  PMID 19102774 · PMC2630979 · BMC medical genetics · 2008 · 8 claims · 6 setups

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  Variation in SYN III distal CpG island methylation is not related to schizophrenia in the population sample or in a monozygotic twin pair discordant for schizophrenia

  brain blood non-human semi-quantitative sodium bisulfite

• 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

• Relationship between the extent of chromosomal losses and the pattern of CpG methylation in gastric carcinomas.

  PMID 16224153 · PMC2779276 · Journal of Korean medical science · 2005 · 7 claims · 4 setups

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  High-level-loss (LOH-H) tumors show a tendency toward unmethylation in Maspin, CAGE, MAGE-A2, and RABGEF1 genes

  microdissected same bisulfite-modified pcr microsatellite methylation-specific bisulfite

• msPIPE: a pipeline for the analysis and visualization of whole-genome bisulfite sequencing data.

  PMID 36123620 · PMC9487059 · BMC bioinformatics · 2022 · 6 claims · 8 setups

  Has reproduction · 100

  msPIPE is a new end-to-end pipeline integrating pre-processing, alignment & methylation calling, and downstream DNA methylation analysis (profiling, HMR, DMR, functional enrichment) with publication-quality figure output for WGBS data

  blood rod sperm old wgbs hypomethylated differential

• Probing the cancer genome.

  PMID 18492227 · PMC2441462 · Genome biology · 2008 · 8 claims · 8 setups

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  Combined Sanger and 454 pyrosequencing of MCF-7 BAC clones identified 157 PCR-confirmed translocation breakpoint junctions, including 10 in-frame junctions confirmed at the transcript level

  mcf-7 tumor lung oral sanger solexa gistic

• The impact of new research technologies on our understanding of environmental causes of disease: the concept of clinical vulnerability.

  PMID 19948053 · PMC2793242 · Environmental health : a global access science source · 2009 · 8 claims · 8 setups

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  GWAS-identified genetic variants confer only modest relative risks (1.15-1.5), comparable in magnitude to weak/contested environmental exposures

  polish cohort nonsmokers low genome-wide biomarker epidemiological

• Investigating epigenetic biomarkers of age, sex, and disease in captive South African cheetahs (Acinonyx jubatus jubatus).

  PMID 41528985 · PMC12798976 · PloS one · 2026 · 8 claims · 7 setups

  Has reproduction · 58

  A cheetah-specific epigenetic clock (CheetahClock) built from 52 CpG sites predicts age across blood and liver samples with r=0.97 and MAE=0.86 years

  cheetah genes methylation elastic epigenome-wide

• 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

• Quantitative epigenetic co-variation in CpG islands and co-regulation of developmental genes.

  PMID 23999385 · PMC6505400 · Scientific reports · 2013 · 8 claims · 8 setups

  Has reproduction · 95

  Four epigenetic modifications (DNA methylation, H3K4me2, H3K4me3, H3K27me3) in mouse CGIs undergo combinatorial variation (co-variation) across ESCs, NPCs and adult brain during neuron differentiation.

  embryonic escs dem-cgis demg methylation chip-seq gene

• Gbdmr: identifying differentially methylated CpG regions in the human genome via generalized beta regressions.

  PMID 38443825 · PMC10916021 · BMC bioinformatics · 2024 · 8 claims · 4 setups

  Has reproduction · 62

  gbdmr models DNA methylation levels of CpG sites using a generalized beta distribution instead of assuming normality as in linear-regression-based methods

  simulated birth gene simulation methylation

• Methylation of class II transactivator gene promoter IV is not associated with susceptibility to multiple sclerosis.

  PMID 18606010 · PMC2464579 · BMC medical genetics · 2008 · 6 claims · 4 setups

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  Methylation of the MHC2TA promoter pIV is not associated with MS susceptibility; no methylation was detected in any twin sample regardless of disease status

  peripheral mhc2ta pcr sanger bisulfite cpg

• Hierarchical classification-based pan-cancer methylation analysis to classify primary cancer.

  PMID 38066424 · PMC10709847 · BMC bioinformatics · 2023 · 8 claims · 8 setups

  Has reproduction · 83

  CHCT, a two-tier hierarchical classification tool built from methylation data, accurately classifies primary cancer type across 30 cancer types.

  tumor clinical methylation clustered methylation unsupervised anova

• Human epigenome project--up and running.

  PMID 14691553 · PMC300691 · PLoS biology · 2003 · 7 claims · 4 setups

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  Epigenetic modifications (e.g., DNA methylation) rather than DNA sequence differences explain phenotypic differences between genetically identical individuals, such as monozygotic twins or inbred mice.

  expressed bat8 genetically methylation genome-wide phenotypic

• DNA methylation profiling of the human major histocompatibility complex: a pilot study for the human epigenome project.

  PMID 15550986 · PMC529316 · PLoS biology · 2004 · 8 claims · 3 setups

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  The human MHC methylation profile is strongly bimodal, with the vast majority of analysed regions being either hypo- (≤30%) or hypermethylated (≥70%)

  mhc subset heterogeneously bisulphite maldi-ms sub-cloning

• 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

• 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

• A novel role for mitochondria in regulating epigenetic modification in the nucleus.

  PMID 18458531 · PMC2639623 · Cancer biology & therapy · 2008 · 8 claims · 6 setups

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  Mitochondria regulate epigenetic (DNA methylation) modification in the nucleus

  mcf12a mda-mb-435 143b restriction western bisulfite