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CluGene: A Bioinformatics Framework for the Identification of Co-Localized, Co-Expressed and Co-Regulated Genes Aimed at the Investigation of Transcriptional Regulatory Networks from High-Throughput Expression Data

Dottorini, Tania; Palladino, Pietro; Senin, Nicola; Persampieri, Tania; Spaccapelo, Roberta; Crisanti, Andrea

CluGene: A Bioinformatics Framework for the Identification of Co-Localized, Co-Expressed and Co-Regulated Genes Aimed at the Investigation of Transcriptional Regulatory Networks from High-Throughput Expression Data Thumbnail


Authors

Pietro Palladino

Nicola Senin

Tania Persampieri

Roberta Spaccapelo

Andrea Crisanti



Contributors

Christian Sch�nbach
Editor

Abstract

The full understanding of the mechanisms underlying transcriptional regulatory networks requires unravelling of complex causal relationships. Genome high-throughput technologies produce a huge amount of information pertaining gene expression and regulation; however, the complexity of the available data is often overwhelming and tools are needed to extract and organize the relevant information. This work starts from the assumption that the observation of co-occurrent events (in particular co-localization, co-expression and co-regulation) may provide a powerful starting point to begin unravelling transcriptional regulatory networks. Co-expressed genes often imply shared functional pathways; co-expressed and functionally related genes are often co-localized, too; moreover, co-expressed and co-localized genes are also potential targets for co-regulation; finally, co-regulation seems more frequent for genes mapped to proximal chromosome regions. Despite the recognized importance of analysing co-occurrent events, no bioinformatics solution allowing the simultaneous analysis of co-expression, co-localization and co-regulation is currently available. Our work resulted in developing and valuating CluGene, a software providing tools to analyze multiple types of co-occurrences within a single interactive environment allowing the interactive investigation of combined co-expression, co-localization and co-regulation of genes. The use of CluGene will enhance the power of testing hypothesis and experimental approaches aimed at unravelling transcriptional regulatory networks. The software is freely available at

Citation

Dottorini, T., Palladino, P., Senin, N., Persampieri, T., Spaccapelo, R., & Crisanti, A. (2013). CluGene: A Bioinformatics Framework for the Identification of Co-Localized, Co-Expressed and Co-Regulated Genes Aimed at the Investigation of Transcriptional Regulatory Networks from High-Throughput Expression Data. PLoS ONE, 8(6), doi:10.1371/journal.pone.0066196

Journal Article Type Article
Acceptance Date May 5, 2012
Online Publication Date Jun 18, 2013
Publication Date Jun 18, 2013
Deposit Date Feb 20, 2019
Publicly Available Date Mar 7, 2019
Journal PLoS ONE
Publisher Public Library of Science
Peer Reviewed Peer Reviewed
Volume 8
Issue 6
Article Number e66196
DOI https://doi.org/10.1371/journal.pone.0066196
Public URL https://nottingham-repository.worktribe.com/output/1570900
Publisher URL https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0066196

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