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  • Automatic Markup of Three-dimensional Chromatin Structures for Hi-C Contact Maps of Dictyostelium discoideum: loops and topologically associated domains

Automatic Markup of Three-dimensional Chromatin Structures for Hi-C Contact Maps of Dictyostelium discoideum: loops and topologically associated domains

Student: Savostianov Anton

Supervisor: Mikhail S. Gelfand

Faculty: Faculty of Computer Science

Educational Programme: Data Analysis for Biology and Medicine (Master)

Final Grade: 8

Year of Graduation: 2019

Current work aims to automatically predict structural units of the chromatin spatial arrangement —— chromatin loops —— in case of social amoeba Dictyostelium discoideum by contact maps from the Hi-C experiment. Despite the functional importance of the DNA folding, developed for mammals prediction methods are not applicable for other species. This work introduces the prediction algorithm based on classical computer vision approaches: Laplacian of Gaussian and Image enhancement. Results' quality is assessed towards the existing manual layout (with ~80% success rate); optimal parameter choice is conducted targeting statistics of produced loop distribution. FDR is proposed to be estimated by fitting with gamma-distribution. As a result, we state that in case of entering hostile environment and transfering to a multicellular slug, there is tendency of loop enlarging and subsequent vanishing.

Full text (added May 22, 2019)

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