Consistency tests for a recursive multi-scale 3D chromatin structure reconstruction algorithm

Caudai C, Salerno E, Zoppè M, Tonazzini A

Computational biology  Chromatin structure  Chromosome conformation capture  LIFE AND MEDICAL SCIENCES. Biology and genetics 

In this report, we test the consistency and coherence of an algorithm obtained as an extension of a technique we proposed in the past. This implements a recursive multi-scale reconstruction of the 3d chromatin structure from Chromosome Conformation Capture data. These data derive from millions of cells, so we cannot expect that they lead to a unique solution; for this reason, we adopt a statistic approach to sample the space of the solutions generated by a suitable objective function, in order to achieve congurations compatible with the input data and the known constraints. The consistency of the algorithm has been tested by producing a large number of results and evaluating the dispersion of the nal values of the objective function. Using the same solutions, synthetic contact matrices have been produced and compared with the input matrix to test the coherence of our solutions with the initial data. Furthermore, we investigated the presence of typical structures in the solutions by hierarchical clustering.