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Int. J. Mol. Sci. 2013, 14(11), 23160-23187; doi:10.3390/ijms141123160

Systems Biology Approach to the Dissection of the Complexity of Regulatory Networks in the S. scrofa Cardiocirculatory System

1
Department of Biology, University of Padova, Via G. Colombo 3, Padova 35121, Italy
2
C.R.I.B.I. Biotechnology Centre, University of Padova, Via U. Bassi 58/B, Padova 35121, Italy
*
Authors to whom correspondence should be addressed.
Received: 9 August 2013 / Revised: 23 October 2013 / Accepted: 2 November 2013 / Published: 21 November 2013
(This article belongs to the Special Issue Regulation by non-coding RNAs 2013)
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Abstract

Genome-wide experiments are routinely used to increase the understanding of the biological processes involved in the development and maintenance of a variety of pathologies. Although the technical feasibility of this type of experiment has improved in recent years, data analysis remains challenging. In this context, gene set analysis has emerged as a fundamental tool for the interpretation of the results. Here, we review strategies used in the gene set approach, and using datasets for the pig cardiocirculatory system as a case study, we demonstrate how the use of a combination of these strategies can enhance the interpretation of results. Gene set analyses are able to distinguish vessels from the heart and arteries from veins in a manner that is consistent with the different cellular composition of smooth muscle cells. By integrating microRNA elements in the regulatory circuits identified, we find that vessel specificity is maintained through specific miRNAs, such as miR-133a and miR-143, which show anti-correlated expression with their mRNA targets.
Keywords: pathway analysis; miRNA; cardiocirculatory; network reconstruction; integrative analysis; pig; artery; vein; vessel pathway analysis; miRNA; cardiocirculatory; network reconstruction; integrative analysis; pig; artery; vein; vessel
This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

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MDPI and ACS Style

Martini, P.; Sales, G.; Calura, E.; Brugiolo, M.; Lanfranchi, G.; Romualdi, C.; Cagnin, S. Systems Biology Approach to the Dissection of the Complexity of Regulatory Networks in the S. scrofa Cardiocirculatory System. Int. J. Mol. Sci. 2013, 14, 23160-23187.

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