Presnted by Jonas Paulsen
Jonas Paulsen 1, Tonje G. Lien 2, Geir Kjetil Sandve 3,4, Lars Holden5, Ørnulf Borgan2, Ingrid K. Glad 2 and Eivind Hovig 1,3,6
1 Oslo University Hospital, Section for Medical Informatics, The Norwegian Radium Hospital, P.O. Box 4950, Nydalen, N-0424 Oslo, Norway.
2 University of Oslo, Department of Mathematics, P.O. Box 1053, Blindern, 0316 Oslo, Norway.
3 University of Oslo, Department of Informatics, P.O. Box 1080, Blindern, 0316 Oslo, Norway.
4 Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, P.O. Box 4950, Nydalen, 0424 Oslo, Norway.
5 Statistics for Innovation, Norwegian Computing Center, 0314 Oslo, Norway.
6 Oslo University Hospital, Institute for Cancer Research, Department of Tumor Biology, The Norwegian Radium Hospital, P.O. Box 4950, Nydalen, N-0424 Oslo, Norway.
The study of chromatin 3D structure has recently gained much focus due to novel techniques, such as Hi-C and Chia-PET, for detecting genome wide chromatin contacts utilizing next-generation sequencing. Both the representation and analysis of such data is complex, and appropriate tools are presently lacking.
We are developing user-friendly tools for statistical analysis of 3D interaction data in a Galaxy framework, building on existing software components of the Genomic HyperBrowser. Our main focus has been on developing hypothesis tests and descriptive statistics where the user can ask specific questions concerning the spatial arrangement of genomic elements in three dimensions.
We show examples of spatial co-localization of chromatin states and fusion transcripts, and show how visualization and descriptive statistics can accompany hypothesis testing to gain biological knowledge of the 3D organization of chromatin.