title: How interacting pathways are regulated by miRNAs in breast cancer subtypes.
abstract: BACKGROUND
  An important challenge in cancer biology is to understand the complex aspects of the disease. It is increasingly evident that genes are not isolated from each other and the comprehension of how different genes are related to each other could explain biological mechanisms causing diseases. Biological pathways are important tools to reveal gene interaction and reduce the large number of genes to be studied by partitioning it into smaller paths. Furthermore, recent scientific evidence has proven that a combination of pathways, instead than a single element of the pathway or a single pathway, could be responsible for pathological changes in a cell.
  
  
  RESULTS
  In this paper we develop a new method that can reveal miRNAs able to regulate, in a coordinated way, networks of gene pathways. We applied the method to subtypes of breast cancer. The basic idea is the identification of pathways significantly enriched with differentially expressed genes among the different breast cancer subtypes and normal tissue. Looking at the pairs of pathways that were found to be functionally related, we created a network of dependent pathways and we focused on identifying miRNAs that could act as miRNA drivers in a coordinated regulation process.
  
  
  CONCLUSIONS
  Our approach enables miRNAs identification that could have an important role in the development of breast cancer.
authors.affiliation: Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy.
authors.forename: Claudia
authors.initials: C
authors.lastname: Cava
authors.affiliation: Interuniversity Institute of Bioinformatics in Brussels (IB), Brussels, Belgium.|Machine Learning Group, ULB, Brussels, Belgium.
authors.forename: Antonio
authors.initials: A
authors.lastname: Colaprico
authors.affiliation: Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy.
authors.forename: Gloria
authors.initials: G
authors.lastname: Bertoli
authors.affiliation: Interuniversity Institute of Bioinformatics in Brussels (IB), Brussels, Belgium.|Machine Learning Group, ULB, Brussels, Belgium.
authors.forename: Gianluca
authors.initials: G
authors.lastname: Bontempi
authors.affiliation: Department of Informatics, Systems and Communications, University of Milan-Bicocca, Milan, Italy.
authors.forename: Giancarlo
authors.initials: G
authors.lastname: Mauri
authors.affiliation: Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy. isabella.castiglioni@ibfm.cnr.it.
authors.forename: Isabella
authors.initials: I
authors.lastname: Castiglioni
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics* / Q000378:metabolism; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods; D053263:Gene Regulatory Networks; D023281:Genomics / Q000379:methods*; D006801:Humans; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism
chemical_list: D035683:MicroRNAs
keywords: Breast cancer; Network of pathways; Pathway cross-talk; miRNAs