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A global abstract analysis of selected histone-modifying enzymes using AKS
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With over 8.4 million PubMed abstracts and with 1000s of new abstracts added daily, it is physically impossible for any conscientious researcher to keep current with all of the newly published research. Most scientists rely on simple information-retrieval techniques to obtain scientific articles pertaining to a topic of interest. However, new sophisticated software programs have been developed to try to understand how biological concepts in scientific literature are used and how these concepts correspond to the query term provided by the user. When searching PubMed abstracts, most life science researchers do not want to be experts in text mining techniques, but simply want to have an all-encompassing understanding of the published information about a biomolecule and its relationship to disease or other biological entities. Therefore, global abstract analysis (GAA) is a novel approach for examining the complexity of information described in PubMed abstracts.

GAA was employed to illustrate how this technique can help uncover additional biological relationships, scientific information, and overall publication trends of a particular collection of biomolecules. In this study we selected twelve histone-modifying enzymes (1). They are important because several common post-translational modifications are driven by these types of histone-modifying enzymes. These resulting modifications influence the structure of chromatin and the dynamic interaction of transcriptional machinery. The modifications include: methylation, demethylation, acetylation, deacetylation, ubiquitination, sumoylation and phosphorylation. Methylation and acetylation are the typical control points between switching from gene silencing to active transcription, whereas hyperacetylated histone tails are associated with active transcription. In addition, ubiquitination is implicated in transcriptional regulation by polycomb silencing and regulation of chromatin structure, while phosphorylated residues on histone tails can be markers for chromatin condensation in mitosis, DNA repair, or apoptosis.

Distinct from traditional simple text search methods, the technique of GAA gives an extensive overview and historical synopsis of the published knowledge of these fascinating histone-modifying enzymes. In this report we describe the application of GAA to a group of disease-associated enzymes and demonstrate how a complete GAA can be developed for any targeted collection of biomolecules for pathway construction, biomarker discovery, or early investigative studies.

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