PUMA
Istituto di Scienza e Tecnologie dell'Informazione     
Caudai C., Salerno E., Zoppè M., Tonazzini A. Consistency tests for a recursive multi-scale 3D chromatin structure reconstruction algorithm. Modellazione e analisi statistica di segnali e immagini in genomica e systems biology. Project report WP1-CNR-ISTI, 2016.
 
 
Abstract
(English)
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 con gurations 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.
Subject Computational biology
Chromatin structure
Chromosome conformation capture
J.3 LIFE AND MEDICAL SCIENCES. Biology and genetics


Icona documento 1) Download Document PDF


Icona documento Open access Icona documento Restricted Icona documento Private

 


Per ulteriori informazioni, contattare: Librarian http://puma.isti.cnr.it

Valid HTML 4.0 Transitional