Abstract
Epigenetics refers to stable and long-term alterations of cellular traits that are not caused by changes in the DNA sequence per se. Rather, covalent modifications of DNA and histones affect gene expression and genome stability via proteins that recognize and act upon such modifications. Many enzymes that catalyse epigenetic modifications or are critical for enzymatic complexes have been discovered, and this is encouraging investigators to study the role of these proteins in diverse normal and pathological processes. Rapidly growing knowledge in the area has resulted in the need for a resource that compiles, organizes and presents curated information to the researchers in an easily accessible and user-friendly form. Here we present EpiFactors, a manually curated database providing information about epigenetic regulators, their complexes, targets and products. EpiFactors contains information on 815 proteins, including 95 histones and protamines. For 789 of these genes, we include expressions values across several samples, in particular a collection of 458 human primary cell samples (for approximately 200 cell types, in many cases from three individual donors), covering most mammalian cell steady states, 255 different cancer cell lines (representing approximately 150 cancer subtypes) and 134 human postmortem tissues. Expression values were obtained by the FANTOM5 consortium using Cap Analysis of Gene Expression technique. EpiFactors also contains information on 69 protein complexes that are involved in epigenetic regulation. The resource is practical for a wide range of users, including biologists, pharmacologists and clinicians.Database URL: http://epifactors.autosome.ru
Highlights
Epigenetics has emerged as an extremely fast-growing area of biomedical research
We present EpiFactors; a database encompassing detailed and curated information about 815 proteins and 69 complexes involved in epigenetic regulation
It is worth noting that some epigenetic factors are transcription factors (TFs) and can bind DNA in a sequencespecific manner. If such sequence preferences are known we provide an external link to a corresponding entry of the HOCOMOCO database, which contains curated models of sequence-specific transcriptional factor binding sites (TFBS) [62]
Summary
Epigenetics has emerged as an extremely fast-growing area of biomedical research. The term ‘epigenetics’ covers DNA and histone modifications, as well as chromatin remodeling. Vol 2015, Article ID bav067 contains information on 69 protein complexes that are involved in epigenetic regulation. Those databases incorporate information on histones and histone-modifying enzymes and include other proteins affecting the chromatin structure without direct histone modifications.
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