title: Analysis of miRNA, mRNA, and TF interactions through network-based methods.
abstract: Recent findings have elucidated that the regulation of messenger RNA (mRNA) levels is due to the synergistic and antagonist actions of transcription factors (TFs) and microRNAs (miRNAs). Mutual interactions among these molecules are easily modeled and analyzed using graphs whose nodes are molecules, and directed edges represent the associations among them. In particular, small subgraphs having three nodes also referred to as feed-forward loops (FFLs) or regulatory loops play a crucial role in many different diseases, such as cancer. Available technological platforms enable the investigation of only a single aspect of these mechanisms, e.g., the quantification of levels of mRNA or miRNA. Consequently, there exist different data sources for investigating some aspects of this problem, e.g., miRNA-mRNA or TF-mRNA associations. The comprehensive analysis is made possible only by the integration and the analysis of these data sources. Currently, the interest of researchers in this area is growing, the number of projects is increasing, and the number of challenges and issues for computer scientists is considerable. The need for an introductive survey from a computer science point of view consequently arises. This survey starts by discussing general concepts related to production of data. Then, main existing approaches of analysis are presented and discussed. Future improvements and challenges are also discussed.
authors.affiliation: Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy.
authors.forename: Pietro H
authors.initials: PH
authors.lastname: Guzzi
authors.affiliation: Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, Catanzaro, Italy.
authors.forename: Maria Teresa
authors.initials: MT
authors.lastname: Di Martino
authors.affiliation: Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, Catanzaro, Italy.
authors.forename: Pierosandro
authors.initials: P
authors.lastname: Tagliaferri
authors.affiliation: Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, Catanzaro, Italy.|Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA USA.
authors.forename: Pierfrancesco
authors.initials: P
authors.lastname: Tassone
authors.affiliation: Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy.
authors.forename: Mario
authors.initials: M
authors.lastname: Cannataro
keywords: Data integration; Network analysis; Transcription factor; mRNA; miRNA