title: Systems biology approach to the dissection of the complexity of regulatory networks in the S. scrofa cardiocirculatory system.
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.
authors.affiliation: Department of Biology, University of Padova, Via G. Colombo 3, Padova 35121, Italy. chiara.romualdi@unipd.it.
authors.forename: Paolo
authors.initials: P
authors.lastname: Martini
authors.forename: Gabriele
authors.initials: G
authors.lastname: Sales
authors.forename: Enrica
authors.initials: E
authors.lastname: Calura
authors.forename: Mattia
authors.initials: M
authors.lastname: Brugiolo
authors.forename: Gerolamo
authors.initials: G
authors.lastname: Lanfranchi
authors.forename: Chiara
authors.initials: C
authors.lastname: Romualdi
authors.forename: Stefano
authors.initials: S
authors.lastname: Cagnin
mesh_terms: D000818:Animals; D001158:Arteries / Q000254:growth & development / Q000378:metabolism; D003331:Coronary Vessels / Q000378:metabolism; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D006801:Humans; D053858:Metabolic Networks and Pathways; D035683:MicroRNAs / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics; D034421:Sus scrofa / Q000235:genetics* / Q000254:growth & development; D049490:Systems Biology; D014680:Veins / Q000254:growth & development / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger