Motivated by an interest to understand how information is organized within genomes, and how genes communicate between each other in the transcription process, in this paper we propose a novel network based methodology for genomic sequence analysis, specifically applied to three organisms: Nanoarchaeum equitans, Escherichia coli, and Saccaromyces cerevisiae. A dictionary based approach previously introduced is here continued through a repeat analysis in genic and intergenic regions. Key results of this work have been found in a biological and computational analysis of novel parametrized gene networks, defined by means of motifs of fixed length occurring inside multiple genes. Cliques emerge as groups of genes sharing a long repeat with a clear biological interpretation, while a (complete, paralog) cluster analysis has outlined some unexpected regularity. Repeat sharing gene networks may be applied in contexts of comparative genomics, as an investigation methodology for a comprehension of evolutional and functional properties of genes.

A genome analysis based on repeat sharing gene networks

CASTELLINI, ALBERTO;FRANCO, Giuditta;MILANESE, ALESSIO
2015-01-01

Abstract

Motivated by an interest to understand how information is organized within genomes, and how genes communicate between each other in the transcription process, in this paper we propose a novel network based methodology for genomic sequence analysis, specifically applied to three organisms: Nanoarchaeum equitans, Escherichia coli, and Saccaromyces cerevisiae. A dictionary based approach previously introduced is here continued through a repeat analysis in genic and intergenic regions. Key results of this work have been found in a biological and computational analysis of novel parametrized gene networks, defined by means of motifs of fixed length occurring inside multiple genes. Cliques emerge as groups of genes sharing a long repeat with a clear biological interpretation, while a (complete, paralog) cluster analysis has outlined some unexpected regularity. Repeat sharing gene networks may be applied in contexts of comparative genomics, as an investigation methodology for a comprehension of evolutional and functional properties of genes.
2015
Genome analysis, Computational genomics, Comparative genomics, Infogenomics, Dictionaries, Repeat frequency, k-mer cluster, Gene networks, Paralog analysis, information theory, Text mining
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11562/902385
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