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PubMeth specifications


Unique identifier OMICS_03768
Name PubMeth
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Allowed
Maintained Yes


  • Primates
    • Homo sapiens

Publication for PubMeth

PubMeth citations


Salivary DNA methylation panel to diagnose HPV positive and HPV negative head and neck cancers

BMC Cancer
PMCID: 5034533
PMID: 27663357
DOI: 10.1186/s12885-016-2785-0

[…] h factor betas (TGFβs) []. TGFβs play a role in cellular regulation, proliferation and differentiation []. As such, PCQAP/MED15 may have an important role as a tumour-suppressor gene []. According to PubMeth database (Ghent University, Ghent, Kortrijk, Belgium), PCQAP/MED15 is hypermethylated in over 66 % of oesophageal and 40 % of prostate cancers. This gene contains two annotated CpG islands, on […]


NEpiC: a network assisted algorithm for epigenetic studies using mean and variance combined signals

Nucleic Acids Res
PMCID: 5027497
PMID: 27302130
DOI: 10.1093/nar/gkw546

[…] there are 16, 2, 11 and 1 genes that have been reported to be differentially methylated in cancers according to a cancer methylation database developed by combining text-mining and expert annotation (Pubmeth) () (Table Part I). According to CGC (), there are 26, 12, 10 and 11 genes that have been causally implicated with cancers, respectively (Table Part I). NEpiC has the highest percentages of […]


Event extraction for DNA methylation

J Biomed Semantics
PMCID: 3239302
PMID: 22166595
DOI: 10.1186/2041-1480-2-S5-S2

[…] st set, giving 100 abstracts for training, 34 for development, and 66 for final test. The splits were performed randomly, but sampling so that each set has an equal number of abstracts drawn from the PubMeth and PubMed subcorpora.The EventMine system has a single tunable threshold parameter that controls the tradeoff between system precision and recall. We first set the tradeoff using a sparse sea […]


The apoptotic machinery as a biological complex system: analysis of its omics and evolution, identification of candidate genes for fourteen major types of cancer, and experimental validation in CML and neuroblastoma

BMC Med Genomics
PMCID: 2683874
PMID: 19402918
DOI: 10.1186/1755-8794-2-20

[…] of AM genes clusters: these were displayed with MeV4.2 []. The information on cancer-related gene mutations was obtained by screening the database Cosmic []. Cancer-related methylation data were from PubMeth []. […]


Linking genes to literature: text mining, information extraction, and retrieval applications for biology

Genome Biol
PMCID: 2559992
PMID: 18834499
DOI: 10.1186/gb-2008-9-s2-s8

[…] easing interest in studying epigenetic modifications of the human genome and its association with diseases such as cancer motivated the development of two other online tools, namely MeInfoText [] and PubMeth [], which use text-mining to provide detailed information on gene methylation and association with cancer. Knowledge about the subcellular location of proteins can provide meaningful contextua […]


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PubMeth institution(s)
Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Laboratory for Bioinformatics and Computational Genomics, Ghent University, Ghent, Belgium

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