Abstract
BackgroundIn epigenetics, the change of the combination of histone modifications at the same genomic location during cell differentiation is of great interest for understanding the function of these modifications and their combinations. Besides analyzing them locally for individual genomic locations or globally using correlations between different cells types, intermediate level analyses of these changes are of interest. More specifically, the different distributions of these combinations for different cell types, respectively, are compared to gain new insights.Results and discussionWe propose a new tool called ‘Masakari’ that allows segmenting genomes based on lists of ranges having a certain property, e.g., peaks describing histone modifications. It provides a graphical user interface allowing to select all data sets and setting all parameters needed for the segmentation process. Moreover, the graphical user interface provides statistical graphics allowing to assess the quality and suitability of the segmentation and the selected data.ConclusionMasakari provides statistics based visualizations and thus fosters insights into the combination of histone modification marks on genome ranges, and the differences of the distribution of these combinations between different cell types.
Highlights
In epigenetics, the change of the combination of histone modifications at the same genomic location during cell differentiation is of great interest for understanding the function of these modifications and their combinations
We propose a new tool called ‘Masakari’ that allows segmenting genomes based on lists of ranges having a certain property, e.g., peaks describing histone modifications
Masakari provides statistics based visualizations and fosters insights into the combination of histone modification marks on genome ranges, and the differences of the distribution of these combinations between different cell types
Summary
The change of the combination of histone modifications at the same genomic location during cell differentiation is of great interest for understanding the function of these modifications and their combinations. Besides analyzing them locally for individual genomic locations or globally using correlations between different cells types, intermediate level analyses of these changes are of interest. While H3K4me correlates positively with the expression of genes and euchromatin formation, H3K27me induces heterochromatin formation and repression of transcription. Promoters associated with both marks are in the so-called poised chromatin state, i.e., transcription is repressed but can be switched on when needed [1,2,3]
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