Confident gene activity prediction based on single histone modification H2BK5ac in human cell lines
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- 作者：Fereshteh Chitsazian ; Mehdi Sadeghi ; Elahe Elahi
- 关键词：Histone modifications ; Transcription ; CART ; MDR ; H2BK5ac
- 刊名：BMC Bioinformatics
- 出版年：2017
- 出版时间：December 2017
- 年：2017
- 卷：18
- 期：1
- 全文大小：2869KB
- 刊物主题：Bioinformatics; Microarrays; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Algorithms;
- 出版者：BioMed Central
- ISSN：1471-2105
- 卷排序：18
文摘
BackgroundThe histones in the core of nucleosomes may be subject to covalent post-transcriptional modifications. These modifications are thought to correlate with and possibly affect various genomic functions, including transcription. Each modification may alone or in combination with other modifications influence or be influenced by transcription. We aimed to identify correlations between single modifications or combinations of modifications at specific nucleosome sized gene regions with transcription activity based on global histone modification and transcription data of human CD4+ T cells and three other human cell lines. Transcription activity was defined in a binary fashion as either on or off. The analysis was done using the Classification and Regression Tree (CART) data mining protocol, and the Multifactorial Dimensionality Reduction (MDR) method was performed to confirm the CART results. These powerful methods have not previously been used for analysis of histone modification data.