title: Infinity: An In-Silico Tool for Genome-Wide Prediction of Specific DNA Matrices in miRNA Genomic Loci.
abstract: BACKGROUND
  miRNAs are potent regulators of gene expression and modulate multiple cellular processes in physiology and pathology. Deregulation of miRNAs expression has been found in various cancer types, thus, miRNAs may be potential targets for cancer therapy. However, the mechanisms through which miRNAs are regulated in cancer remain unclear. Therefore, the identification of transcriptional factor-miRNA crosstalk is one of the most update aspects of the study of miRNAs regulation.
  
  
  RESULTS
  In the present study we describe the development of a fast and user-friendly software, named infinity, able to find the presence of DNA matrices, such as binding sequences for transcriptional factors, on ~65kb (kilobase) of 939 human miRNA genomic sequences, simultaneously. Of note, the power of this software has been validated in vivo by performing chromatin immunoprecipitation assays on a subset of new in silico identified target sequences (CCAAT) for the transcription factor NF-Y on colon cancer deregulated miRNA loci. Moreover, for the first time, we have demonstrated that NF-Y, through its CCAAT binding activity, regulates the expression of miRNA-181a, -181b, -21, -17, -130b, -301b in colon cancer cells.
  
  
  CONCLUSIONS
  The infinity software that we have developed is a powerful tool to underscore new TF/miRNA regulatory networks.
  
  
  METHODS
  Infinity was implemented in pure Java using Eclipse framework, and runs on Linux and MS Windows machine, with MySQL database. The software is freely available on the web at https://github.com/bio-devel/infinity. The website is implemented in JavaScript, PHP and HTML with all major browsers supported.
authors.affiliation: Department of Research, Advanced Diagnostics, and Technological Innovation, Regina Elena National Cancer Institute, Rome, Italy.
authors.forename: Emmanuela
authors.initials: E
authors.lastname: Falcone
authors.affiliation: Department of Information Engineering, Electronics and Telecommunications (DIET), Faculty of Information Engineering, Statistics and Informatics, University Sapienza, Rome, Italy.
authors.forename: Luca
authors.initials: L
authors.lastname: Grandoni
authors.affiliation: Department of Research, Advanced Diagnostics, and Technological Innovation, Regina Elena National Cancer Institute, Rome, Italy.
authors.forename: Francesca
authors.initials: F
authors.lastname: Garibaldi
authors.affiliation: Department of Research, Advanced Diagnostics, and Technological Innovation, Regina Elena National Cancer Institute, Rome, Italy.
authors.forename: Isabella
authors.initials: I
authors.lastname: Manni
authors.affiliation: Department of Information Engineering, Electronics and Telecommunications (DIET), Faculty of Information Engineering, Statistics and Informatics, University Sapienza, Rome, Italy.
authors.forename: Giancarlo
authors.initials: G
authors.lastname: Filligoi
authors.affiliation: Department of Research, Advanced Diagnostics, and Technological Innovation, Regina Elena National Cancer Institute, Rome, Italy.
authors.forename: Giulia
authors.initials: G
authors.lastname: Piaggio
authors.affiliation: Department of Research, Advanced Diagnostics, and Technological Innovation, Regina Elena National Cancer Institute, Rome, Italy.
authors.forename: Aymone
authors.initials: A
authors.lastname: Gurtner
mesh_terms: D000465:Algorithms; D023081:CCAAT-Binding Factor / Q000737:chemistry; D045744:Cell Line, Tumor; D003110:Colonic Neoplasms / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000737:chemistry; D015972:Gene Expression Regulation, Neoplastic; D015894:Genome, Human; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D011381:Programming Languages; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D012984:Software
chemical_list: D023081:CCAAT-Binding Factor; D035683:MicroRNAs; D004247:DNA