title: Predicting microRNA modulation in human prostate cancer using a simple String IDentifier (SID1.0).
abstract: To make faster and efficient the identification of mRNA targets common to more than one miRNA, and to identify new miRNAs modulated in specific pathways, a computer program identified as SID1.0 (simple String IDentifier) was developed and successfully applied in the identification of deregulated miRNAs in prostate cancer cells. This computationally inexpensive Fortran program is based on the strategy of exhaustive search and specifically designed to screen shared data (target genes, miRNAs and pathways) available from PicTar and DIANA-MicroT 3.0 databases. As far as we know this is the first software designed to filter data retrieved from available miRNA databases. SID1.0 takes advantage of the standard Fortran intrinsic functions for manipulating text strings and requires ASCII input files. In order to demonstrate SID1.0 applicability, some miRNAs expected from the literature to associate with cancerogenesis (miR-125b, miR-148a and miR-141), were randomly identified as main entries for SID1.0 to explore matching sequences of mRNA targets and also to explore KEGG pathways for the presence of ID codes of targeted genes. Besides genes and pathways already described in the literature, SID1.0 has proven to useful for predicting other genes involved in prostate carcinoma. These latter were used to identify new deregulated miRNAs: miR-141, miR-148a, miR-19a and miR-19b. Prediction data were preliminary confirmed by expression analysis of the identified miRNAs in androgen-dependent (LNCaP) and independent (PC3) prostate carcinoma cell lines and in normal prostatic epithelial cells (PrEC).
authors.affiliation: Dipartimento di Scienze Biomolecolari, Sezione di Biochimica e Biologia molecolare, Università degli Studi di Urbino "Carlo Bo", Urbino, Italy. maria.albertini@uniurb.it
authors.forename: Maria C
authors.initials: MC
authors.lastname: Albertini
authors.forename: Fabiola
authors.initials: F
authors.lastname: Olivieri
authors.forename: Raffaella
authors.initials: R
authors.lastname: Lazzarini
authors.forename: Francesca
authors.initials: F
authors.lastname: Pilolli
authors.forename: Francesco
authors.initials: F
authors.lastname: Galli
authors.forename: Giorgio
authors.initials: G
authors.lastname: Spada
authors.forename: Augusto
authors.initials: A
authors.lastname: Accorsi
authors.forename: Maria R
authors.initials: MR
authors.lastname: Rippo
authors.forename: Antonio D
authors.initials: AD
authors.lastname: Procopio
mesh_terms: D000465:Algorithms; D045744:Cell Line, Tumor; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D006801:Humans; D008297:Male; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism*; D011471:Prostatic Neoplasms / Q000235:genetics* / Q000378:metabolism*; D015203:Reproducibility of Results; D012984:Software
chemical_list: D035683:MicroRNAs