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.
%0 Journal Article
%1 Zeckzer2020-wr
%A Zeckzer, Dirk
%A Hausdorf, Alrik
%A Hinzmann, Nicole
%A Müller, Lydia
%A Wiegreffe, Daniel
%D 2020
%I Springer Science and Business Media LLC
%J BMC Bioinformatics
%K Cell ChIP-seq; Chromatin Histone development; modifications state;
%N 1
%P 437
%T Masakari: visualization supported statistical analysis of genome segmentations
%V 21
%X 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.
@article{Zeckzer2020-wr,
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.},
added-at = {2024-09-10T11:54:51.000+0200},
author = {Zeckzer, Dirk and Hausdorf, Alrik and Hinzmann, Nicole and M{\"u}ller, Lydia and Wiegreffe, Daniel},
biburl = {https://puma.scadsai.uni-leipzig.de/bibtex/2ef59ef28bada0c3fde0f242d6506c819/scadsfct},
copyright = {http://creativecommons.org/licenses/by/4.0/},
interhash = {b67275c08a7f9bea05aab5628b7c1832},
intrahash = {ef59ef28bada0c3fde0f242d6506c819},
journal = {BMC Bioinformatics},
keywords = {Cell ChIP-seq; Chromatin Histone development; modifications state;},
language = {en},
month = oct,
number = 1,
pages = 437,
publisher = {Springer Science and Business Media LLC},
timestamp = {2024-09-10T11:54:51.000+0200},
title = {Masakari: visualization supported statistical analysis of genome segmentations},
volume = 21,
year = 2020
}
