Masakari: visualization supported statistical analysis of genome segmentations
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Masakari: visualization supported statistical analysis of genome segmentations Dirk Zeckzer3*† , Alrik Hausdorf3†, Nicole Hinzmann3, Lydia Müller1,2 and Daniel Wiegreffe2,3 *Correspondence: zeckzer@informatik. uni‑leipzig.de † Alrik Hausdorf and Nicole Hinzmann contributed equally to this work. 3 Image and Signal Processing Group, Department of Computer Science, University of Leipzig, Augustusplatz 10, 04109 Leipzig, Germany Full list of author information is available at the end of the article
Abstract Background: 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. 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 discussion: 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. 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. Conclusion: Masakari 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. Keywords: ChIP-seq, Chromatin state, Histone modifications, Cell development
Background Every cell of an organism carries the same genome. However, each cell type shows a specific expression pattern. Epigenetic modifications were found to regulate the gene expression. Prominent examples are the trimethylations of the lysines of histone H3 at position 4 (H3K4me3) and at position 27 (H3K27me3) located near the transcription start sites of genes. While H3K4me3 correlates positively with the expression of genes and euchromatin formation, H3K27me3 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 easily be switched on when needed [1–3]. Early research showed, that changes in the combination of marks occur frequently during development. Thus, they shape the cell type identity. Often, changes at the promoters are tracked and correlated with cell expression. However, some modifications do © The Author(s) 2020. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproducti
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