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Publication for PubMeth
Salivary DNA methylation panel to diagnose HPV positive and HPV negative head and neck cancers
[…] 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
[…] 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
[…] 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
[…] 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
[…] 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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