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  1. Pubblicazioni

NuChart-II: a graph-based approach for the analysis and interpretation of Hi-C data

Contributo in Atti di convegno
Data di Pubblicazione:
2015
Abstract:
Long-range chromosomal associations between genomic regions, and their repositioning in the 3D space of the nucleus, are now considered to be key contributors to the regulation of gene expressions, and important links have been highlighted with other genomic features involved in DNA rearrangements. Recent Chromosome Conformation Capture (3C) measurements performed with high throughput sequencing (Hi-C) and molecular dynamics studies show that there is a large correlation between co-localization and co-regulation of genes, but these important researches are hampered by the lack of biologists-friendly analysis and visualisation software. In this work we present NuChart-II, a software that allows the user to annotate and visualize a list of input genes with information relying on Hi-C data, integrating knowledge data about genomic features that are involved in the chromosome spatial organization. This software works directly with sequenced reads to identify related Hi-C fragments, with the aim of creating gene-centric neighbourhood graphs on which multi-omics features can be mapped. NuChart-II is a highly optimized implementation of a previous prototype package developed in R, in which the graph-based representation of Hi-C data was tested. The prototype showed inevitable problems of scalability while working genome-wide on large datasets: particular attention has been paid in optimizing the data structures employed while constructing the neighbourhood graph, so as to foster an efficient parallel implementation of the software. The normalization of Hi-C data has been modified and improved, in order to provide a reliable estimation of proximity likelihood for the genes.
Tipologia CRIS:
04A-Conference paper in volume
Keywords:
fastflow, bioinformatics
Elenco autori:
Tordini, Fabio; Drocco, Maurizio; Merelli, Ivan; Milanes, Luciano; Liò, Pietro; Aldinucci, Marco.
Autori di Ateneo:
ALDINUCCI Marco
Link alla scheda completa:
https://iris.unito.it/handle/2318/1522044
Link al Full Text:
https://iris.unito.it/retrieve/handle/2318/1522044/40627/2014_nuchart_cibb.pdf
Titolo del libro:
LNCS post conference proceedings of the Eleventh International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics CIBB 2014
Pubblicato in:
LECTURE NOTES IN COMPUTER SCIENCE
Journal
LECTURE NOTES IN COMPUTER SCIENCE
Series
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URL

http://calvados.di.unipi.it/storage/paper_files/2014_nuchart_cibb.pdf
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